From n.binns at ed.ac.uk Fri Jun 3 06:58:04 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 11:58:04 +0100 Subject: [EMBOSS] Primer3/Clustalw compatibility with EMBOSS v6.3.1 Message-ID: <4DE8BE3C.4070905@ed.ac.uk> Hi, 1. Is Primer 3 v1.1.4 still the recommended version to be used with Jemboss/EMBOSS? I seem to remember that the latest release (v2.2.3) is currently incompatible with EMBOSS v6.3.1 2. Is Clustalw v2.1 compatible with EMBOSS v6.3.1 or should I use the previous version (v2.0.12)? 3. EMBOSS v6.3.1 is about 10 months old now. Has development on EMBOSS ceased? Many thanks for your help. Nigel -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From n.binns at ed.ac.uk Fri Jun 3 06:51:40 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 11:51:40 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 Message-ID: <4DE8BCBC.3080209@ed.ac.uk> Hi, I'm getting a warning message indicating that /usr/include/gd.h does not exist on my system at the point in the Jemboss install script (install-jemboss-server.sh) that refers to the libpng and gd libraries. I confirmed that gd.h does not exist on our server with a system-wide search. I'm attempting to install EMBOSS/Jemboss v6.3.1 onto a server running Red Hat Enterprise Linux 6.0 Server 64-bit (fully patched). I have confirmed that I have the following relevant RPMs installed: libpng-1.2.44-1.el6.x86_64.rpm libpng-devel-1.2.44-1.el6.x86_64.rpm gd-2.0.35-10.el6.x86_64.rpm On our system, the following files are located in the indicated directories: /usr/include/png.h /usr/lib64/libpng.so (plus some other libpng files such as libpng12.so) /usr/lib64/libgd.so.2 A search via our Red Hat Network subscription indicates that there are no other gd RPMs available, such as gd-devel. I've tried pointing the installation script at the /usr/lib64 directory using the --with-pngdriver flag when requested, but this leads to another warning saying that /usr/lib64/include/png.h does not exist. I appreciate that I could just compile and install the libpng and gd libraries from the two project's websites (in fact I've confirmed that gd.h is present in the gd-2.0.35.tar.gz distribution), however, I would prefer that Jemboss used the distro-provided libraries, as these will be updated automatically via its package management system. Many thanks for your help. Nigel -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From uludag at ebi.ac.uk Fri Jun 3 08:00:52 2011 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 03 Jun 2011 13:00:52 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8BCBC.3080209@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> Message-ID: <1307102452.29447.13.camel@emboss1.ebi.ac.uk> Hi Nigel, I have gd.x86_64 installed in my machine which looks like the source for the gd.h file I have. Can you please check whether you have this package installed. Regards Mahmut From uludag at ebi.ac.uk Fri Jun 3 08:05:01 2011 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 03 Jun 2011 13:05:01 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8BCBC.3080209@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> Message-ID: <1307102701.29447.15.camel@emboss1.ebi.ac.uk> > have confirmed that I have the following relevant RPMs installed: > > libpng-1.2.44-1.el6.x86_64.rpm > libpng-devel-1.2.44-1.el6.x86_64.rpm > gd-2.0.35-10.el6.x86_64.rpm Apologies, i just have noticed you already have the equivalent of gd.x86_64, gd-2.0.35-10.el6.x86_64.rpm installed. Mahmut From n.binns at ed.ac.uk Fri Jun 3 08:45:03 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 13:45:03 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <1307102701.29447.15.camel@emboss1.ebi.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> Message-ID: <4DE8D74F.7020009@ed.ac.uk> Hi Mahmut, What do you suggest I do? Is there another source of gd.h? Would this have anything to do with the LD_LIBRARY_PATH environment variable? I've looked at /etc/ld.so.conf and run ldconfig -v, but ultimately, if the file isn't present, then whether or not it's being pointed to is largely irrelevant. Best regards, Nigel On 03/06/2011 13:05, Mahmut Uludag wrote: >> have confirmed that I have the following relevant RPMs installed: >> >> libpng-1.2.44-1.el6.x86_64.rpm >> libpng-devel-1.2.44-1.el6.x86_64.rpm >> gd-2.0.35-10.el6.x86_64.rpm > Apologies, i just have noticed you already have the equivalent of > gd.x86_64, gd-2.0.35-10.el6.x86_64.rpm installed. > > Mahmut -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From uludag at ebi.ac.uk Fri Jun 3 09:08:44 2011 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 03 Jun 2011 14:08:44 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8D74F.7020009@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> <4DE8D74F.7020009@ed.ac.uk> Message-ID: <1307106524.29447.24.camel@emboss1.ebi.ac.uk> Hi Nigel, I have discovered that I have gd-devel package also installed on my machine and it is the source of gd.h file i have. I found this using the "rpm -q gd-devel -l" command as suggested on the following page. http://old.nabble.com/GD-Install-Trouble-td18948476.html In your first email you said Red Hat Network doesn't have gd-devel, my linux knowledge is not good, it might be reasonable to double check whether this package is really not available in Red Hat Network. Regards Mahmut From n.binns at ed.ac.uk Fri Jun 3 09:25:01 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 14:25:01 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <5FAE4EF51F20774D9C21A133494A3FE013C19646DB@LESMBX1.adf.bham.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> <4DE8D74F.7020009@ed.ac.uk> <5FAE4EF51F20774D9C21A133494A3FE013C19646DB@LESMBX1.adf.bham.ac.uk> Message-ID: <4DE8E0AD.4060804@ed.ac.uk> Hi Tony, Many thanks for your reply. I also get the same response on our system when I run whatprovides, i.e. 'No matches found'. I have have raised a support ticket with Red Hat through our subscription to RHN. Hopefully they will resolve this issue shortly by releasing a devel RPM (e.g. gd-devel-2.0.35-10.el6.x86_64.rpm) containing the missing gd.h file. Best regards, Nigel On 03/06/2011 14:08, Anthony Pemberton wrote: > Nigel, > > It looks as if this header is not available under RHEL 6. Very strange?? I agree with you there should be a gd-devel rpm. I am pretty sure this was the case in previous RHEL releases. The "devel" rpms normally contain the headers for compilation using the libraries. I have done a > > # yum whatprovides '*/include/gd.h' > > On my 64 bit RHEL 6 system and the header is nowhere to be found in the repo. Hmm? > > Regards, > > Tony P. > > > -----Original Message----- > From:emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Nigel Binns > Sent: 03 June 2011 13:45 > To: Mahmut Uludag > Cc:emboss at emboss.open-bio.org > Subject: Re: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 > > Hi Mahmut, > > What do you suggest I do? Is there another source of gd.h? > > Would this have anything to do with the LD_LIBRARY_PATH environment > variable? I've looked at /etc/ld.so.conf and run ldconfig -v, but > ultimately, if the file isn't present, then whether or not it's being > pointed to is largely irrelevant. > > Best regards, > > Nigel > > On 03/06/2011 13:05, Mahmut Uludag wrote: >>> have confirmed that I have the following relevant RPMs installed: >>> >>> libpng-1.2.44-1.el6.x86_64.rpm >>> libpng-devel-1.2.44-1.el6.x86_64.rpm >>> gd-2.0.35-10.el6.x86_64.rpm >> Apologies, i just have noticed you already have the equivalent of >> gd.x86_64, gd-2.0.35-10.el6.x86_64.rpm installed. >> >> Mahmut -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From n.binns at ed.ac.uk Fri Jun 3 09:42:33 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 14:42:33 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <49186.82.26.12.214.1307107955.squirrel@imap04.ebi.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <49186.82.26.12.214.1307107955.squirrel@imap04.ebi.ac.uk> Message-ID: <4DE8E4C9.1090804@ed.ac.uk> Hi Alan, Many thanks. gd-devel-2.0.35-10.el6.x86_64.rpm is indeed available in the Optional Server channel. Our RHN subscription permits us to access it. Hopefully this will solve the problem. Again, many thanks for your help. It is much appreciated. Best regards, Nigel On 03/06/2011 14:32, ajb at ebi.ac.uk wrote: > I believe that gd-devel for RHEL6 can be obtained by subscribing to their > 'optional' channel. > > Unfamiliarity with RHEL prevents me from saying how that is done > but it could conceivably cost money. > > HTH > > Alan (on holiday so further replies unlikely until next week). > > >> Hi, >> >> I'm getting a warning message indicating that /usr/include/gd.h does not >> exist on my system at the point in the Jemboss install script >> (install-jemboss-server.sh) that refers to the libpng and gd libraries. >> I confirmed that gd.h does not exist on our server with a system-wide >> search. I'm attempting to install EMBOSS/Jemboss v6.3.1 onto a server >> running Red Hat Enterprise Linux 6.0 Server 64-bit (fully patched). I >> have confirmed that I have the following relevant RPMs installed: >> >> libpng-1.2.44-1.el6.x86_64.rpm >> libpng-devel-1.2.44-1.el6.x86_64.rpm >> gd-2.0.35-10.el6.x86_64.rpm >> >> On our system, the following files are located in the indicated >> directories: >> /usr/include/png.h >> /usr/lib64/libpng.so (plus some other libpng files such as libpng12.so) >> /usr/lib64/libgd.so.2 >> >> A search via our Red Hat Network subscription indicates that there are >> no other gd RPMs available, such as gd-devel. >> >> I've tried pointing the installation script at the /usr/lib64 directory >> using the --with-pngdriver flag when requested, but this leads to >> another warning saying that /usr/lib64/include/png.h does not exist. >> >> I appreciate that I could just compile and install the libpng and gd >> libraries from the two project's websites (in fact I've confirmed that >> gd.h is present in the gd-2.0.35.tar.gz distribution), however, I would >> prefer that Jemboss used the distro-provided libraries, as these will be >> updated automatically via its package management system. >> >> Many thanks for your help. >> >> Nigel >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From n.binns at ed.ac.uk Fri Jun 3 09:34:44 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 14:34:44 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <1307106524.29447.24.camel@emboss1.ebi.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> <4DE8D74F.7020009@ed.ac.uk> <1307106524.29447.24.camel@emboss1.ebi.ac.uk> Message-ID: <4DE8E2F4.5070006@ed.ac.uk> Hi Mahmut, I ran the command you provide and got the response: package gd-devel is not installed. I checked RHN again and can confirm that there is no such RPM package (i.e. a devel version) available for our system (Red Hat Enterprise Linux Server release 6.1 (Santiago) 64-bit). I'm probably being incredibly naive, but do you think it would work if I manually copied the gd.h file from the gd distribution tarball (obtained directly from the GD project website) into the /usr/include directory? Best regards, Nigel On 03/06/2011 14:08, Mahmut Uludag wrote: > Hi Nigel, > > I have discovered that I have gd-devel package also installed on my > machine and it is the source of gd.h file i have. I found this using the > "rpm -q gd-devel -l" command as suggested on the following page. > > http://old.nabble.com/GD-Install-Trouble-td18948476.html > > In your first email you said Red Hat Network doesn't have gd-devel, my > linux knowledge is not good, it might be reasonable to double check > whether this package is really not available in Red Hat Network. > > Regards > Mahmut -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From bene at hkl.hms.harvard.edu Fri Jun 3 10:22:19 2011 From: bene at hkl.hms.harvard.edu (Ben Eisenbraun) Date: Fri, 3 Jun 2011 10:22:19 -0400 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8E2F4.5070006@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> <4DE8D74F.7020009@ed.ac.uk> <1307106524.29447.24.camel@emboss1.ebi.ac.uk> <4DE8E2F4.5070006@ed.ac.uk> Message-ID: <20110603142217.GA1275@crystal.harvard.edu> Hi Nigel, > I checked RHN again and can confirm that there is no such RPM package > (i.e. a devel version) available for our system (Red Hat Enterprise > Linux Server release 6.1 (Santiago) 64-bit). > > I'm probably being incredibly naive, but do you think it would work if I > manually copied the gd.h file from the gd distribution tarball (obtained > directly from the GD project website) into the /usr/include directory? That won't work. Just install the RPM from Scientific Linux 6: http://mirror.anl.gov/pub/scientific-linux/6.0/x86_64/os/Packages/gd-devel-2.0.35-10.el6.x86_64.rpm -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | From n.binns at ed.ac.uk Fri Jun 3 10:45:22 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 15:45:22 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8E4C9.1090804@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <49186.82.26.12.214.1307107955.squirrel@imap04.ebi.ac.uk> <4DE8E4C9.1090804@ed.ac.uk> Message-ID: <4DE8F382.2090907@ed.ac.uk> This solved the problem. After handling the dependencies associated with gd-devel-2.0.35-10.el6.x86_64.rpm, I'm in the process of running the Jemboss install script and this time all png/gd libraries were detected and compilation of EMBOSS has started. Many thanks for all your help resolving this. Nigel On 03/06/2011 14:42, Nigel Binns wrote: > Hi Alan, > > Many thanks. gd-devel-2.0.35-10.el6.x86_64.rpm is indeed available in > the Optional Server channel. Our RHN subscription permits us to access > it. Hopefully this will solve the problem. > > Again, many thanks for your help. It is much appreciated. > > Best regards, > > Nigel > > On 03/06/2011 14:32, ajb at ebi.ac.uk wrote: >> I believe that gd-devel for RHEL6 can be obtained by subscribing to >> their >> 'optional' channel. >> >> Unfamiliarity with RHEL prevents me from saying how that is done >> but it could conceivably cost money. >> >> HTH >> >> Alan (on holiday so further replies unlikely until next week). >> >> >>> Hi, >>> >>> I'm getting a warning message indicating that /usr/include/gd.h does >>> not >>> exist on my system at the point in the Jemboss install script >>> (install-jemboss-server.sh) that refers to the libpng and gd libraries. >>> I confirmed that gd.h does not exist on our server with a system-wide >>> search. I'm attempting to install EMBOSS/Jemboss v6.3.1 onto a server >>> running Red Hat Enterprise Linux 6.0 Server 64-bit (fully patched). I >>> have confirmed that I have the following relevant RPMs installed: >>> >>> libpng-1.2.44-1.el6.x86_64.rpm >>> libpng-devel-1.2.44-1.el6.x86_64.rpm >>> gd-2.0.35-10.el6.x86_64.rpm >>> >>> On our system, the following files are located in the indicated >>> directories: >>> /usr/include/png.h >>> /usr/lib64/libpng.so (plus some other libpng files such as libpng12.so) >>> /usr/lib64/libgd.so.2 >>> >>> A search via our Red Hat Network subscription indicates that there are >>> no other gd RPMs available, such as gd-devel. >>> >>> I've tried pointing the installation script at the /usr/lib64 directory >>> using the --with-pngdriver flag when requested, but this leads to >>> another warning saying that /usr/lib64/include/png.h does not exist. >>> >>> I appreciate that I could just compile and install the libpng and gd >>> libraries from the two project's websites (in fact I've confirmed that >>> gd.h is present in the gd-2.0.35.tar.gz distribution), however, I would >>> prefer that Jemboss used the distro-provided libraries, as these >>> will be >>> updated automatically via its package management system. >>> >>> Many thanks for your help. >>> >>> Nigel >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> _______________________________________________ >>> EMBOSS mailing list >>> EMBOSS at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/emboss >>> >> > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From heikki.salavirta at helsinki.fi Wed Jun 22 08:53:25 2011 From: heikki.salavirta at helsinki.fi (Heikki Salavirta) Date: Wed, 22 Jun 2011 15:53:25 +0300 Subject: [EMBOSS] anarchistic results in einverted Message-ID: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> Hello, I've been running einverted queries with the same sequence, with the only difference in parameters being max repeat (e.g. 1000, 2000, 4000, 6000, 8000, 10000 & 20000). Other parameters are gap: 12, threshold: 50, match: 3 & mismatch: -4. I'd expect that this would result in an ever increasing number of results, as the max repeat parameter increases. However, this is not what I'm seeing. E.g. when max repeat is 2000, there are 3 results from the sequence prior to >10kb loci. It's the same result when max repeat is 4000. However, when max repeat is 6000, there are 2 results prior to >10kb loci, and 1 of them is not reported by 2000 & 4000 queries. In this particular result the gap between the inverted repeats is only 2 nucleotides! When max repeat is 8000, there's only 1 result prior to >10kb loci, which is also reported by 2000, 4000 & 6000 queries. When max repeat is 1000, there are 4 results prior to >10kb loci. Could somebody perhaps explain these unexpected result, and perhaps suggest proper parameters for finding all inverted repeats from a >150kb sequence. Thanks, -heikki -- +358505416697 | heikki.salavirta at helsinki.fi From pmr at ebi.ac.uk Wed Jun 22 10:30:26 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 22 Jun 2011 15:30:26 +0100 Subject: [EMBOSS] anarchistic results in einverted In-Reply-To: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> References: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> Message-ID: <4E01FC82.8000300@ebi.ac.uk> dear Heikki, On 06/22/11 13:53, Heikki Salavirta wrote: > Hello, > > I've been running einverted queries with the same sequence, with the > only difference in parameters being max repeat (e.g. 1000, 2000, 4000, > 6000, 8000, 10000 & 20000). Other parameters are gap: 12, threshold: 50, > match: 3 & mismatch: -4. > > I'd expect that this would result in an ever increasing number of > results, as the max repeat parameter increases. However, this is not > what I'm seeing. We have some fixes to einverted in the next release. Can you please send your input sequence to me so I can test what the results are from the new version. regards, Peter Rice EMBOSS Team From pmr at ebi.ac.uk Thu Jun 23 05:03:43 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 23 Jun 2011 10:03:43 +0100 Subject: [EMBOSS] anarchistic results in einverted In-Reply-To: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> References: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> Message-ID: <4E03016F.60605@ebi.ac.uk> Hi Heikki, On 06/22/11 13:53, Heikki Salavirta wrote: > Hello, > > I've been running einverted queries with the same sequence, with the > only difference in parameters being max repeat (e.g. 1000, 2000, 4000, > 6000, 8000, 10000 & 20000). Other parameters are gap: 12, threshold: 50, > match: 3 & mismatch: -4. > > I'd expect that this would result in an ever increasing number of > results, as the max repeat parameter increases. However, this is not > what I'm seeing. > > E.g. when max repeat is 2000, there are 3 results from the sequence > prior to >10kb loci. > > It's the same result when max repeat is 4000. > > However, when max repeat is 6000, there are 2 results prior to >10kb > loci, and 1 of them is not reported by 2000 & 4000 queries. In this > particular result the gap between the inverted repeats is only 2 > nucleotides! > > When max repeat is 8000, there's only 1 result prior to >10kb loci, > which is also reported by 2000, 4000 & 6000 queries. > > When max repeat is 1000, there are 4 results prior to >10kb loci. > > Could somebody perhaps explain these unexpected result, and perhaps > suggest proper parameters for finding all inverted repeats from a >150kb > sequence. einverted was designed for the annotation of the Caenorhabditis elegans genome. It deliberately does not find all inverted repeats. The algorithm searches the max repeat region and reports the highest scoring repeat. It can also report other high scoring repeats in the region, but only if they are not already covered by a result. We have changed the way the overlapping scores in the max repeats region are detected (there was a problem in the original program when repeat traceback went over the end of the region) but it should not significantly change the number of reported hits. As to finding all inverted repeats ... I think that is not possible with einverted because it uses a dynamic programming approach and will fail to find overlapping repeats. We would be interested in any other algorithms we could implement if there are no open source applications available for them. Hope this helps Peter Rice EMBOSS Team From d.m.a.martin at dundee.ac.uk Fri Jun 24 06:01:31 2011 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Fri, 24 Jun 2011 11:01:31 +0100 Subject: [EMBOSS] The EMBOSS book Message-ID: <4E046E8B020000E000015A44@ia-gw-6.dundee.ac.uk> It is good to see the EMBOSS books finally appearing. Is the user guide based (at least in part) on my Admin guide of several years ago, or the EMBOSS tutorial that I extended from Val Curwen's original? ..d -- David Martin PhD College of Life Sciences University of Dundee 01382 388704 The University of Dundee is a Scottish Registered Charity, No. SC015096. ************************************************************ Please consider the environment. Do you really need to print this email? The University of Dundee is a registered Scottish charity, No: SC015096 From mathog at caltech.edu Mon Jun 27 17:12:58 2011 From: mathog at caltech.edu (David Mathog) Date: Mon, 27 Jun 2011 14:12:58 -0700 Subject: [EMBOSS] Build -m32 on 64 bit host, problems Message-ID: Found it in configure. There is a test to see if the compiling system is x86_64, but there doesn't seem to be anything there to see if the intent is to build 32 bit on that system. Chopped out that test and reran configure, which removed the -D__amd64__ from the makefiles. Compiling now. Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Mon Jun 27 17:06:44 2011 From: mathog at caltech.edu (David Mathog) Date: Mon, 27 Jun 2011 14:06:44 -0700 Subject: [EMBOSS] Build -m32 on 64 bit host, problems Message-ID: Trying again to compile Emboss 6.3.1. Attempting to build 32 bit versions as most of the target machines run that, however, the compiler is running on a 64 bit OS. Download 6.3.1, unpack, apply 1-4 patch. Then in top level: export CFLAGS="-march=athlon-mp -m32" ./configure --prefix=/usr/common which all went fine, except that: grep m32 Makefile CFLAGS = -march=athlon-mp -m32 -O2 -DNO_AUTH -D__amd64__ I don't see how to reconcile __amd64__ with the other flags. Is there some switch that can be thrown in ./configure to correct this? Note, I really do want the 32 bit version even on the 64 bit system, so that all of the machines will be running exactly the same version. Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Mon Jun 27 17:49:09 2011 From: mathog at caltech.edu (David Mathog) Date: Mon, 27 Jun 2011 14:49:09 -0700 Subject: [EMBOSS] Build -m32 on 64 bit host, problems Message-ID: > Found it in configure. Ack, make that, "found it in _every_ configure". Rather than hand editing these, modified the lot of them to break the x86_64 test, so it will fail even if the strings are present (or use sed): find . | \ grep configure$ | extract -fmt 'extract -in [1,] -out /tmp/foo -rtds "grep x86_64" -rtss "grep WILLNOTMATCH"; /bin/cp /tmp/foo [1,]' | \ execinput Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Tue Jun 28 16:02:11 2011 From: mathog at caltech.edu (David Mathog) Date: Tue, 28 Jun 2011 13:02:11 -0700 Subject: [EMBOSS] Graphics glitch emboss 3.6.1 Message-ID: Finally built 3.6.1 for 32 bits on a 64 bit machine and verified that it runs there and on 32 bit machines (all linux). There is however an odd graphics glitch wherever it runs. For instance: pepwheel -sequence=test -sbegin=1 -send=353 -graph=X11 results in a graph that is similar to that on another system (6.0.1 on Solaris) but has: 1: thicker lines 2. diamonds that don't close. They look like this (ascii art, used a fixed space font) ^ / \ / \ + / / __v That is, if the start is at the "+" and has coords (x1,y1) and the point v has coords (xv,yv), then it looks like the line that is supposed to go back to (x1,y1), goes instead to (x1,yv). Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Tue Jun 28 16:25:02 2011 From: mathog at caltech.edu (David Mathog) Date: Tue, 28 Jun 2011 13:25:02 -0700 Subject: [EMBOSS] Graphics glitch emboss 3.6.1 Message-ID: Found it. in ajgraph.c starting at line 2760: xa[0] = x; ya[0] = y + incr; xa[1] = x + incr; ya[1] = y + size; xa[2] = x + size; ya[2] = y + incr; xa[3] = x + incr; ya[3] = y; xa[4] = x; ya[4] = y; the last line should be ya[4] = y + incr; Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From pmr at ebi.ac.uk Wed Jun 29 03:34:52 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 29 Jun 2011 08:34:52 +0100 Subject: [EMBOSS] Graphics glitch emboss 3.6.1 In-Reply-To: References: Message-ID: <4E0AD59C.8090807@ebi.ac.uk> Hi David, On 28/06/2011 21:25, David Mathog wrote: > Found it. in ajgraph.c starting at line 2760: Great. Thanks for that one. Peter From n.binns at ed.ac.uk Fri Jun 3 10:58:04 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 11:58:04 +0100 Subject: [EMBOSS] Primer3/Clustalw compatibility with EMBOSS v6.3.1 Message-ID: <4DE8BE3C.4070905@ed.ac.uk> Hi, 1. Is Primer 3 v1.1.4 still the recommended version to be used with Jemboss/EMBOSS? I seem to remember that the latest release (v2.2.3) is currently incompatible with EMBOSS v6.3.1 2. Is Clustalw v2.1 compatible with EMBOSS v6.3.1 or should I use the previous version (v2.0.12)? 3. EMBOSS v6.3.1 is about 10 months old now. Has development on EMBOSS ceased? Many thanks for your help. Nigel -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From n.binns at ed.ac.uk Fri Jun 3 10:51:40 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 11:51:40 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 Message-ID: <4DE8BCBC.3080209@ed.ac.uk> Hi, I'm getting a warning message indicating that /usr/include/gd.h does not exist on my system at the point in the Jemboss install script (install-jemboss-server.sh) that refers to the libpng and gd libraries. I confirmed that gd.h does not exist on our server with a system-wide search. I'm attempting to install EMBOSS/Jemboss v6.3.1 onto a server running Red Hat Enterprise Linux 6.0 Server 64-bit (fully patched). I have confirmed that I have the following relevant RPMs installed: libpng-1.2.44-1.el6.x86_64.rpm libpng-devel-1.2.44-1.el6.x86_64.rpm gd-2.0.35-10.el6.x86_64.rpm On our system, the following files are located in the indicated directories: /usr/include/png.h /usr/lib64/libpng.so (plus some other libpng files such as libpng12.so) /usr/lib64/libgd.so.2 A search via our Red Hat Network subscription indicates that there are no other gd RPMs available, such as gd-devel. I've tried pointing the installation script at the /usr/lib64 directory using the --with-pngdriver flag when requested, but this leads to another warning saying that /usr/lib64/include/png.h does not exist. I appreciate that I could just compile and install the libpng and gd libraries from the two project's websites (in fact I've confirmed that gd.h is present in the gd-2.0.35.tar.gz distribution), however, I would prefer that Jemboss used the distro-provided libraries, as these will be updated automatically via its package management system. Many thanks for your help. Nigel -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From uludag at ebi.ac.uk Fri Jun 3 12:00:52 2011 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 03 Jun 2011 13:00:52 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8BCBC.3080209@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> Message-ID: <1307102452.29447.13.camel@emboss1.ebi.ac.uk> Hi Nigel, I have gd.x86_64 installed in my machine which looks like the source for the gd.h file I have. Can you please check whether you have this package installed. Regards Mahmut From uludag at ebi.ac.uk Fri Jun 3 12:05:01 2011 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 03 Jun 2011 13:05:01 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8BCBC.3080209@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> Message-ID: <1307102701.29447.15.camel@emboss1.ebi.ac.uk> > have confirmed that I have the following relevant RPMs installed: > > libpng-1.2.44-1.el6.x86_64.rpm > libpng-devel-1.2.44-1.el6.x86_64.rpm > gd-2.0.35-10.el6.x86_64.rpm Apologies, i just have noticed you already have the equivalent of gd.x86_64, gd-2.0.35-10.el6.x86_64.rpm installed. Mahmut From n.binns at ed.ac.uk Fri Jun 3 12:45:03 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 13:45:03 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <1307102701.29447.15.camel@emboss1.ebi.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> Message-ID: <4DE8D74F.7020009@ed.ac.uk> Hi Mahmut, What do you suggest I do? Is there another source of gd.h? Would this have anything to do with the LD_LIBRARY_PATH environment variable? I've looked at /etc/ld.so.conf and run ldconfig -v, but ultimately, if the file isn't present, then whether or not it's being pointed to is largely irrelevant. Best regards, Nigel On 03/06/2011 13:05, Mahmut Uludag wrote: >> have confirmed that I have the following relevant RPMs installed: >> >> libpng-1.2.44-1.el6.x86_64.rpm >> libpng-devel-1.2.44-1.el6.x86_64.rpm >> gd-2.0.35-10.el6.x86_64.rpm > Apologies, i just have noticed you already have the equivalent of > gd.x86_64, gd-2.0.35-10.el6.x86_64.rpm installed. > > Mahmut -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From uludag at ebi.ac.uk Fri Jun 3 13:08:44 2011 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 03 Jun 2011 14:08:44 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8D74F.7020009@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> <4DE8D74F.7020009@ed.ac.uk> Message-ID: <1307106524.29447.24.camel@emboss1.ebi.ac.uk> Hi Nigel, I have discovered that I have gd-devel package also installed on my machine and it is the source of gd.h file i have. I found this using the "rpm -q gd-devel -l" command as suggested on the following page. http://old.nabble.com/GD-Install-Trouble-td18948476.html In your first email you said Red Hat Network doesn't have gd-devel, my linux knowledge is not good, it might be reasonable to double check whether this package is really not available in Red Hat Network. Regards Mahmut From n.binns at ed.ac.uk Fri Jun 3 13:25:01 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 14:25:01 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <5FAE4EF51F20774D9C21A133494A3FE013C19646DB@LESMBX1.adf.bham.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> <4DE8D74F.7020009@ed.ac.uk> <5FAE4EF51F20774D9C21A133494A3FE013C19646DB@LESMBX1.adf.bham.ac.uk> Message-ID: <4DE8E0AD.4060804@ed.ac.uk> Hi Tony, Many thanks for your reply. I also get the same response on our system when I run whatprovides, i.e. 'No matches found'. I have have raised a support ticket with Red Hat through our subscription to RHN. Hopefully they will resolve this issue shortly by releasing a devel RPM (e.g. gd-devel-2.0.35-10.el6.x86_64.rpm) containing the missing gd.h file. Best regards, Nigel On 03/06/2011 14:08, Anthony Pemberton wrote: > Nigel, > > It looks as if this header is not available under RHEL 6. Very strange?? I agree with you there should be a gd-devel rpm. I am pretty sure this was the case in previous RHEL releases. The "devel" rpms normally contain the headers for compilation using the libraries. I have done a > > # yum whatprovides '*/include/gd.h' > > On my 64 bit RHEL 6 system and the header is nowhere to be found in the repo. Hmm? > > Regards, > > Tony P. > > > -----Original Message----- > From:emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Nigel Binns > Sent: 03 June 2011 13:45 > To: Mahmut Uludag > Cc:emboss at emboss.open-bio.org > Subject: Re: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 > > Hi Mahmut, > > What do you suggest I do? Is there another source of gd.h? > > Would this have anything to do with the LD_LIBRARY_PATH environment > variable? I've looked at /etc/ld.so.conf and run ldconfig -v, but > ultimately, if the file isn't present, then whether or not it's being > pointed to is largely irrelevant. > > Best regards, > > Nigel > > On 03/06/2011 13:05, Mahmut Uludag wrote: >>> have confirmed that I have the following relevant RPMs installed: >>> >>> libpng-1.2.44-1.el6.x86_64.rpm >>> libpng-devel-1.2.44-1.el6.x86_64.rpm >>> gd-2.0.35-10.el6.x86_64.rpm >> Apologies, i just have noticed you already have the equivalent of >> gd.x86_64, gd-2.0.35-10.el6.x86_64.rpm installed. >> >> Mahmut -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From n.binns at ed.ac.uk Fri Jun 3 13:42:33 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 14:42:33 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <49186.82.26.12.214.1307107955.squirrel@imap04.ebi.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <49186.82.26.12.214.1307107955.squirrel@imap04.ebi.ac.uk> Message-ID: <4DE8E4C9.1090804@ed.ac.uk> Hi Alan, Many thanks. gd-devel-2.0.35-10.el6.x86_64.rpm is indeed available in the Optional Server channel. Our RHN subscription permits us to access it. Hopefully this will solve the problem. Again, many thanks for your help. It is much appreciated. Best regards, Nigel On 03/06/2011 14:32, ajb at ebi.ac.uk wrote: > I believe that gd-devel for RHEL6 can be obtained by subscribing to their > 'optional' channel. > > Unfamiliarity with RHEL prevents me from saying how that is done > but it could conceivably cost money. > > HTH > > Alan (on holiday so further replies unlikely until next week). > > >> Hi, >> >> I'm getting a warning message indicating that /usr/include/gd.h does not >> exist on my system at the point in the Jemboss install script >> (install-jemboss-server.sh) that refers to the libpng and gd libraries. >> I confirmed that gd.h does not exist on our server with a system-wide >> search. I'm attempting to install EMBOSS/Jemboss v6.3.1 onto a server >> running Red Hat Enterprise Linux 6.0 Server 64-bit (fully patched). I >> have confirmed that I have the following relevant RPMs installed: >> >> libpng-1.2.44-1.el6.x86_64.rpm >> libpng-devel-1.2.44-1.el6.x86_64.rpm >> gd-2.0.35-10.el6.x86_64.rpm >> >> On our system, the following files are located in the indicated >> directories: >> /usr/include/png.h >> /usr/lib64/libpng.so (plus some other libpng files such as libpng12.so) >> /usr/lib64/libgd.so.2 >> >> A search via our Red Hat Network subscription indicates that there are >> no other gd RPMs available, such as gd-devel. >> >> I've tried pointing the installation script at the /usr/lib64 directory >> using the --with-pngdriver flag when requested, but this leads to >> another warning saying that /usr/lib64/include/png.h does not exist. >> >> I appreciate that I could just compile and install the libpng and gd >> libraries from the two project's websites (in fact I've confirmed that >> gd.h is present in the gd-2.0.35.tar.gz distribution), however, I would >> prefer that Jemboss used the distro-provided libraries, as these will be >> updated automatically via its package management system. >> >> Many thanks for your help. >> >> Nigel >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From n.binns at ed.ac.uk Fri Jun 3 13:34:44 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 14:34:44 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <1307106524.29447.24.camel@emboss1.ebi.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> <4DE8D74F.7020009@ed.ac.uk> <1307106524.29447.24.camel@emboss1.ebi.ac.uk> Message-ID: <4DE8E2F4.5070006@ed.ac.uk> Hi Mahmut, I ran the command you provide and got the response: package gd-devel is not installed. I checked RHN again and can confirm that there is no such RPM package (i.e. a devel version) available for our system (Red Hat Enterprise Linux Server release 6.1 (Santiago) 64-bit). I'm probably being incredibly naive, but do you think it would work if I manually copied the gd.h file from the gd distribution tarball (obtained directly from the GD project website) into the /usr/include directory? Best regards, Nigel On 03/06/2011 14:08, Mahmut Uludag wrote: > Hi Nigel, > > I have discovered that I have gd-devel package also installed on my > machine and it is the source of gd.h file i have. I found this using the > "rpm -q gd-devel -l" command as suggested on the following page. > > http://old.nabble.com/GD-Install-Trouble-td18948476.html > > In your first email you said Red Hat Network doesn't have gd-devel, my > linux knowledge is not good, it might be reasonable to double check > whether this package is really not available in Red Hat Network. > > Regards > Mahmut -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From bene at hkl.hms.harvard.edu Fri Jun 3 14:22:19 2011 From: bene at hkl.hms.harvard.edu (Ben Eisenbraun) Date: Fri, 3 Jun 2011 10:22:19 -0400 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8E2F4.5070006@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <1307102701.29447.15.camel@emboss1.ebi.ac.uk> <4DE8D74F.7020009@ed.ac.uk> <1307106524.29447.24.camel@emboss1.ebi.ac.uk> <4DE8E2F4.5070006@ed.ac.uk> Message-ID: <20110603142217.GA1275@crystal.harvard.edu> Hi Nigel, > I checked RHN again and can confirm that there is no such RPM package > (i.e. a devel version) available for our system (Red Hat Enterprise > Linux Server release 6.1 (Santiago) 64-bit). > > I'm probably being incredibly naive, but do you think it would work if I > manually copied the gd.h file from the gd distribution tarball (obtained > directly from the GD project website) into the /usr/include directory? That won't work. Just install the RPM from Scientific Linux 6: http://mirror.anl.gov/pub/scientific-linux/6.0/x86_64/os/Packages/gd-devel-2.0.35-10.el6.x86_64.rpm -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | From n.binns at ed.ac.uk Fri Jun 3 14:45:22 2011 From: n.binns at ed.ac.uk (Nigel Binns) Date: Fri, 03 Jun 2011 15:45:22 +0100 Subject: [EMBOSS] PNG/GD graphics library issue whilst trying to install EMBOSS/Jemboss v6.3.1 In-Reply-To: <4DE8E4C9.1090804@ed.ac.uk> References: <4DE8BCBC.3080209@ed.ac.uk> <49186.82.26.12.214.1307107955.squirrel@imap04.ebi.ac.uk> <4DE8E4C9.1090804@ed.ac.uk> Message-ID: <4DE8F382.2090907@ed.ac.uk> This solved the problem. After handling the dependencies associated with gd-devel-2.0.35-10.el6.x86_64.rpm, I'm in the process of running the Jemboss install script and this time all png/gd libraries were detected and compilation of EMBOSS has started. Many thanks for all your help resolving this. Nigel On 03/06/2011 14:42, Nigel Binns wrote: > Hi Alan, > > Many thanks. gd-devel-2.0.35-10.el6.x86_64.rpm is indeed available in > the Optional Server channel. Our RHN subscription permits us to access > it. Hopefully this will solve the problem. > > Again, many thanks for your help. It is much appreciated. > > Best regards, > > Nigel > > On 03/06/2011 14:32, ajb at ebi.ac.uk wrote: >> I believe that gd-devel for RHEL6 can be obtained by subscribing to >> their >> 'optional' channel. >> >> Unfamiliarity with RHEL prevents me from saying how that is done >> but it could conceivably cost money. >> >> HTH >> >> Alan (on holiday so further replies unlikely until next week). >> >> >>> Hi, >>> >>> I'm getting a warning message indicating that /usr/include/gd.h does >>> not >>> exist on my system at the point in the Jemboss install script >>> (install-jemboss-server.sh) that refers to the libpng and gd libraries. >>> I confirmed that gd.h does not exist on our server with a system-wide >>> search. I'm attempting to install EMBOSS/Jemboss v6.3.1 onto a server >>> running Red Hat Enterprise Linux 6.0 Server 64-bit (fully patched). I >>> have confirmed that I have the following relevant RPMs installed: >>> >>> libpng-1.2.44-1.el6.x86_64.rpm >>> libpng-devel-1.2.44-1.el6.x86_64.rpm >>> gd-2.0.35-10.el6.x86_64.rpm >>> >>> On our system, the following files are located in the indicated >>> directories: >>> /usr/include/png.h >>> /usr/lib64/libpng.so (plus some other libpng files such as libpng12.so) >>> /usr/lib64/libgd.so.2 >>> >>> A search via our Red Hat Network subscription indicates that there are >>> no other gd RPMs available, such as gd-devel. >>> >>> I've tried pointing the installation script at the /usr/lib64 directory >>> using the --with-pngdriver flag when requested, but this leads to >>> another warning saying that /usr/lib64/include/png.h does not exist. >>> >>> I appreciate that I could just compile and install the libpng and gd >>> libraries from the two project's websites (in fact I've confirmed that >>> gd.h is present in the gd-2.0.35.tar.gz distribution), however, I would >>> prefer that Jemboss used the distro-provided libraries, as these >>> will be >>> updated automatically via its package management system. >>> >>> Many thanks for your help. >>> >>> Nigel >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> _______________________________________________ >>> EMBOSS mailing list >>> EMBOSS at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/emboss >>> >> > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From heikki.salavirta at helsinki.fi Wed Jun 22 12:53:25 2011 From: heikki.salavirta at helsinki.fi (Heikki Salavirta) Date: Wed, 22 Jun 2011 15:53:25 +0300 Subject: [EMBOSS] anarchistic results in einverted Message-ID: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> Hello, I've been running einverted queries with the same sequence, with the only difference in parameters being max repeat (e.g. 1000, 2000, 4000, 6000, 8000, 10000 & 20000). Other parameters are gap: 12, threshold: 50, match: 3 & mismatch: -4. I'd expect that this would result in an ever increasing number of results, as the max repeat parameter increases. However, this is not what I'm seeing. E.g. when max repeat is 2000, there are 3 results from the sequence prior to >10kb loci. It's the same result when max repeat is 4000. However, when max repeat is 6000, there are 2 results prior to >10kb loci, and 1 of them is not reported by 2000 & 4000 queries. In this particular result the gap between the inverted repeats is only 2 nucleotides! When max repeat is 8000, there's only 1 result prior to >10kb loci, which is also reported by 2000, 4000 & 6000 queries. When max repeat is 1000, there are 4 results prior to >10kb loci. Could somebody perhaps explain these unexpected result, and perhaps suggest proper parameters for finding all inverted repeats from a >150kb sequence. Thanks, -heikki -- +358505416697 | heikki.salavirta at helsinki.fi From pmr at ebi.ac.uk Wed Jun 22 14:30:26 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 22 Jun 2011 15:30:26 +0100 Subject: [EMBOSS] anarchistic results in einverted In-Reply-To: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> References: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> Message-ID: <4E01FC82.8000300@ebi.ac.uk> dear Heikki, On 06/22/11 13:53, Heikki Salavirta wrote: > Hello, > > I've been running einverted queries with the same sequence, with the > only difference in parameters being max repeat (e.g. 1000, 2000, 4000, > 6000, 8000, 10000 & 20000). Other parameters are gap: 12, threshold: 50, > match: 3 & mismatch: -4. > > I'd expect that this would result in an ever increasing number of > results, as the max repeat parameter increases. However, this is not > what I'm seeing. We have some fixes to einverted in the next release. Can you please send your input sequence to me so I can test what the results are from the new version. regards, Peter Rice EMBOSS Team From pmr at ebi.ac.uk Thu Jun 23 09:03:43 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 23 Jun 2011 10:03:43 +0100 Subject: [EMBOSS] anarchistic results in einverted In-Reply-To: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> References: <20110622155325.16797dasuxlbkkw5.salavirt@webmail.helsinki.fi> Message-ID: <4E03016F.60605@ebi.ac.uk> Hi Heikki, On 06/22/11 13:53, Heikki Salavirta wrote: > Hello, > > I've been running einverted queries with the same sequence, with the > only difference in parameters being max repeat (e.g. 1000, 2000, 4000, > 6000, 8000, 10000 & 20000). Other parameters are gap: 12, threshold: 50, > match: 3 & mismatch: -4. > > I'd expect that this would result in an ever increasing number of > results, as the max repeat parameter increases. However, this is not > what I'm seeing. > > E.g. when max repeat is 2000, there are 3 results from the sequence > prior to >10kb loci. > > It's the same result when max repeat is 4000. > > However, when max repeat is 6000, there are 2 results prior to >10kb > loci, and 1 of them is not reported by 2000 & 4000 queries. In this > particular result the gap between the inverted repeats is only 2 > nucleotides! > > When max repeat is 8000, there's only 1 result prior to >10kb loci, > which is also reported by 2000, 4000 & 6000 queries. > > When max repeat is 1000, there are 4 results prior to >10kb loci. > > Could somebody perhaps explain these unexpected result, and perhaps > suggest proper parameters for finding all inverted repeats from a >150kb > sequence. einverted was designed for the annotation of the Caenorhabditis elegans genome. It deliberately does not find all inverted repeats. The algorithm searches the max repeat region and reports the highest scoring repeat. It can also report other high scoring repeats in the region, but only if they are not already covered by a result. We have changed the way the overlapping scores in the max repeats region are detected (there was a problem in the original program when repeat traceback went over the end of the region) but it should not significantly change the number of reported hits. As to finding all inverted repeats ... I think that is not possible with einverted because it uses a dynamic programming approach and will fail to find overlapping repeats. We would be interested in any other algorithms we could implement if there are no open source applications available for them. Hope this helps Peter Rice EMBOSS Team From d.m.a.martin at dundee.ac.uk Fri Jun 24 10:01:31 2011 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Fri, 24 Jun 2011 11:01:31 +0100 Subject: [EMBOSS] The EMBOSS book Message-ID: <4E046E8B020000E000015A44@ia-gw-6.dundee.ac.uk> It is good to see the EMBOSS books finally appearing. Is the user guide based (at least in part) on my Admin guide of several years ago, or the EMBOSS tutorial that I extended from Val Curwen's original? ..d -- David Martin PhD College of Life Sciences University of Dundee 01382 388704 The University of Dundee is a Scottish Registered Charity, No. SC015096. ************************************************************ Please consider the environment. Do you really need to print this email? The University of Dundee is a registered Scottish charity, No: SC015096 From mathog at caltech.edu Mon Jun 27 21:12:58 2011 From: mathog at caltech.edu (David Mathog) Date: Mon, 27 Jun 2011 14:12:58 -0700 Subject: [EMBOSS] Build -m32 on 64 bit host, problems Message-ID: Found it in configure. There is a test to see if the compiling system is x86_64, but there doesn't seem to be anything there to see if the intent is to build 32 bit on that system. Chopped out that test and reran configure, which removed the -D__amd64__ from the makefiles. Compiling now. Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Mon Jun 27 21:06:44 2011 From: mathog at caltech.edu (David Mathog) Date: Mon, 27 Jun 2011 14:06:44 -0700 Subject: [EMBOSS] Build -m32 on 64 bit host, problems Message-ID: Trying again to compile Emboss 6.3.1. Attempting to build 32 bit versions as most of the target machines run that, however, the compiler is running on a 64 bit OS. Download 6.3.1, unpack, apply 1-4 patch. Then in top level: export CFLAGS="-march=athlon-mp -m32" ./configure --prefix=/usr/common which all went fine, except that: grep m32 Makefile CFLAGS = -march=athlon-mp -m32 -O2 -DNO_AUTH -D__amd64__ I don't see how to reconcile __amd64__ with the other flags. Is there some switch that can be thrown in ./configure to correct this? Note, I really do want the 32 bit version even on the 64 bit system, so that all of the machines will be running exactly the same version. Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Mon Jun 27 21:49:09 2011 From: mathog at caltech.edu (David Mathog) Date: Mon, 27 Jun 2011 14:49:09 -0700 Subject: [EMBOSS] Build -m32 on 64 bit host, problems Message-ID: > Found it in configure. Ack, make that, "found it in _every_ configure". Rather than hand editing these, modified the lot of them to break the x86_64 test, so it will fail even if the strings are present (or use sed): find . | \ grep configure$ | extract -fmt 'extract -in [1,] -out /tmp/foo -rtds "grep x86_64" -rtss "grep WILLNOTMATCH"; /bin/cp /tmp/foo [1,]' | \ execinput Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Tue Jun 28 20:02:11 2011 From: mathog at caltech.edu (David Mathog) Date: Tue, 28 Jun 2011 13:02:11 -0700 Subject: [EMBOSS] Graphics glitch emboss 3.6.1 Message-ID: Finally built 3.6.1 for 32 bits on a 64 bit machine and verified that it runs there and on 32 bit machines (all linux). There is however an odd graphics glitch wherever it runs. For instance: pepwheel -sequence=test -sbegin=1 -send=353 -graph=X11 results in a graph that is similar to that on another system (6.0.1 on Solaris) but has: 1: thicker lines 2. diamonds that don't close. They look like this (ascii art, used a fixed space font) ^ / \ / \ + / / __v That is, if the start is at the "+" and has coords (x1,y1) and the point v has coords (xv,yv), then it looks like the line that is supposed to go back to (x1,y1), goes instead to (x1,yv). Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Tue Jun 28 20:25:02 2011 From: mathog at caltech.edu (David Mathog) Date: Tue, 28 Jun 2011 13:25:02 -0700 Subject: [EMBOSS] Graphics glitch emboss 3.6.1 Message-ID: Found it. in ajgraph.c starting at line 2760: xa[0] = x; ya[0] = y + incr; xa[1] = x + incr; ya[1] = y + size; xa[2] = x + size; ya[2] = y + incr; xa[3] = x + incr; ya[3] = y; xa[4] = x; ya[4] = y; the last line should be ya[4] = y + incr; Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From pmr at ebi.ac.uk Wed Jun 29 07:34:52 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 29 Jun 2011 08:34:52 +0100 Subject: [EMBOSS] Graphics glitch emboss 3.6.1 In-Reply-To: References: Message-ID: <4E0AD59C.8090807@ebi.ac.uk> Hi David, On 28/06/2011 21:25, David Mathog wrote: > Found it. in ajgraph.c starting at line 2760: Great. Thanks for that one. Peter