From johnston at biochem.ucl.ac.uk Fri Sep 7 07:41:41 2007 From: johnston at biochem.ucl.ac.uk (Caroline Johnston) Date: Fri, 7 Sep 2007 12:41:41 +0100 (BST) Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c Message-ID: Hi, Trying to install the stable EMBOSS package on Ubuntu and although it configures fine make fails with the following error: gd.c: In function 'plD_init_gif_Dev': gd.c:600: error: 'png_Dev' has no member named 'palette' gd.c:601: error: 'png_Dev' has no member named 'truecolour' gd.c: In function 'plD_eop_gif': Google's being no help. Anyone know how to fix the problem? Thanks. Cass From ajb at ebi.ac.uk Fri Sep 7 10:07:57 2007 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 7 Sep 2007 15:07:57 +0100 (BST) Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c In-Reply-To: References: Message-ID: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> Hello Cass, You will get that error if the system thinks that you have a version of the GD libraries less than version 2 on your system. You would do well to check what version of GD (and its associated dev[elopment] package) you have installed. After loading any new GD package onto your system then you'll need to do the EMBOSS './configure' step again. We do not use Ubuntu here but, from memory (which could be wrong), the relevant Ubuntu packages you need will be called something like libgd2 and libgd2-dev. HTH Alan > Hi, > > Trying to install the stable EMBOSS package on Ubuntu and although it > configures fine make fails with the following error: > > gd.c: In function 'plD_init_gif_Dev': > gd.c:600: error: 'png_Dev' has no member named 'palette' > gd.c:601: error: 'png_Dev' has no member named 'truecolour' > gd.c: In function 'plD_eop_gif': > > Google's being no help. Anyone know how to fix the problem? > > Thanks. > > Cass > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From pmr at ebi.ac.uk Fri Sep 7 10:20:13 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 07 Sep 2007 15:20:13 +0100 Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c In-Reply-To: References: Message-ID: <46E15E1D.9000201@ebi.ac.uk> Caroline Johnston wrote: > Trying to install the stable EMBOSS package on Ubuntu and although it > configures fine make fails with the following error: > > gd.c: In function 'plD_init_gif_Dev': > gd.c:600: error: 'png_Dev' has no member named 'palette' > gd.c:601: error: 'png_Dev' has no member named 'truecolour' > gd.c: In function 'plD_eop_gif': What version of libgd do you have installed? We added GIF support which requires a more recent version. regards, Peter Rice From johnston at biochem.ucl.ac.uk Fri Sep 7 10:28:31 2007 From: johnston at biochem.ucl.ac.uk (Caroline Johnston) Date: Fri, 7 Sep 2007 15:28:31 +0100 (BST) Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c In-Reply-To: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> References: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> Message-ID: On Fri, 7 Sep 2007 ajb at ebi.ac.uk wrote: > You will get that error if the system thinks that you have a > version of the GD libraries less than version 2 on your system. Newer versions installed. Seems to be working grand now. Cheers, Cass xx From steffen_moeller at gmx.de Fri Sep 7 10:37:54 2007 From: steffen_moeller at gmx.de (Steffen Moeller) Date: Fri, 7 Sep 2007 16:37:54 +0200 Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c In-Reply-To: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> References: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> Message-ID: <200709071637.54603.steffen_moeller@gmx.de> Hello, There is a Debian package for EMBOSS 5 provided by Charles Plessy of the Debian-Med community that may be directly installable on Ubuntu, too. Please give it a try and be so kind to report. You find more details at http://wiki.debian.org/pkg-emboss. Cheers, Steffen On Friday 07 September 2007 16:07:57 ajb at ebi.ac.uk wrote: > Hello Cass, > > You will get that error if the system thinks that you have a > version of the GD libraries less than version 2 on your system. > > You would do well to check what version of GD (and its associated > dev[elopment] package) you have installed. After loading > any new GD package onto your system then you'll need to > do the EMBOSS './configure' step again. > > We do not use Ubuntu here but, from memory (which could be wrong), the > relevant Ubuntu packages you need will be called something like libgd2 and > libgd2-dev. > > HTH > > Alan > > > Hi, > > > > Trying to install the stable EMBOSS package on Ubuntu and although it > > configures fine make fails with the following error: > > > > gd.c: In function 'plD_init_gif_Dev': > > gd.c:600: error: 'png_Dev' has no member named 'palette' > > gd.c:601: error: 'png_Dev' has no member named 'truecolour' > > gd.c: In function 'plD_eop_gif': > > > > Google's being no help. Anyone know how to fix the problem? > > > > Thanks. > > > > Cass > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part. Url : http://lists.open-bio.org/pipermail/emboss/attachments/20070907/d38dda5e/attachment.bin From Marco.Berg-van-den at DSM.COM Fri Sep 21 07:24:02 2007 From: Marco.Berg-van-den at DSM.COM (Berg-van-den, Marco) Date: Fri, 21 Sep 2007 13:24:02 +0200 Subject: [EMBOSS] question about 'fuzznuc'and whole datases Message-ID: <944926C5F6D8DD4588FDB9307728B9365560F8@nldlf12w3ms001.CORPAD.DSM-GROUP.COM> Hi, I would like to do a pattern search against the whole GenBank or EMBL database. How do I do that within fuzznuc? Or should I use another program for that? Thanks in advance, Marco van den Berg DISCLAIMER: This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. From sufei at mail.sdu.edu.cn Fri Sep 21 09:47:09 2007 From: sufei at mail.sdu.edu.cn (=?gb2312?B?y9Xssw==?=) Date: Fri, 21 Sep 2007 21:47:09 +0800 Subject: [EMBOSS] (no subject) Message-ID: <390382598.22106@mail.sdu.edu.cn> Sorry, I am not familiar with the emboss programs. I am studying, you can ask others. Yours Tonny +++++++++++++++++++++++++++++++++++++++++++++++++++++++= Shandong University The department of life science China ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From Sarah.Vardy at student.griffith.edu.au Tue Sep 25 00:50:37 2007 From: Sarah.Vardy at student.griffith.edu.au (Sarah.Vardy at student.griffith.edu.au) Date: Tue, 25 Sep 2007 14:50:37 +1000 Subject: [EMBOSS] problems installing emboss Message-ID: Hi, I am having some problems installing emboss. When I try to 'make' the installation the error message tells me that aclocal-1.10 is missing. Can anyone tell me how I solve this error? Thank you. Sarah From dalloliogm at gmail.com Wed Sep 26 05:40:10 2007 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Wed, 26 Sep 2007 11:40:10 +0200 Subject: [EMBOSS] problems installing emboss In-Reply-To: References: Message-ID: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> You have to install 'aclocal-1.10'. Why don't you tell us which operating system are you using? Win or Linux? In the latter case, it is possible that there is already a binary package available for your distribution, so you will be able to install emboss without compiling. 2007/9/25, Sarah.Vardy at student.griffith.edu.au : > Hi, > > > > I am having some problems installing emboss. > > > > When I try to 'make' the installation the error message tells me that > aclocal-1.10 is missing. Can anyone tell me how I solve this error? > > > > Thank you. > > > > Sarah > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- ----------------------------------------------------------- My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com From dksamuel at gmail.com Wed Sep 26 06:37:24 2007 From: dksamuel at gmail.com (Duleep Samuel) Date: Wed, 26 Sep 2007 16:07:24 +0530 Subject: [EMBOSS] Fwd: problems installing emboss In-Reply-To: References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> Message-ID: If on windows XP the binary installs like a dream,Samuel On 9/26/07, Giovanni Marco Dall'Olio wrote: > > You have to install 'aclocal-1.10'. > > Why don't you tell us which operating system are you using? Win or Linux? > In the latter case, it is possible that there is already a binary > package available for your distribution, so you will be able to > install emboss without compiling. > > > > 2007/9/25, Sarah.Vardy at student.griffith.edu.au > : > > Hi, > > > > > > > > I am having some problems installing emboss. > > > > > > > > When I try to 'make' the installation the error message tells me that > > aclocal-1.10 is missing. Can anyone tell me how I solve this error? > > > > > > > > Thank you. > > > > > > > > Sarah > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > -- > ----------------------------------------------------------- > > My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From andrespinzon at gmail.com Wed Sep 26 10:54:30 2007 From: andrespinzon at gmail.com (Andres Pinzon) Date: Wed, 26 Sep 2007 09:54:30 -0500 Subject: [EMBOSS] problems installing emboss In-Reply-To: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> Message-ID: <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> "aclocal" is part of the "automake" utility in GNU/linux, maybe you dont have this installed. Check if it is in your system, just type "automake" in any console.:-) Cheers, On 9/26/07, Giovanni Marco Dall'Olio wrote: > You have to install 'aclocal-1.10'. -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From golharam at umdnj.edu Wed Sep 26 11:14:19 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 26 Sep 2007 11:14:19 -0400 Subject: [EMBOSS] problems installing emboss In-Reply-To: <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> Message-ID: <46FA774B.7070604@umdnj.edu> Alternatively, you can install EMBOSS from the pre-built RPMS, http://informatics.umdnj.edu/BioRPMs Andres Pinzon wrote: > "aclocal" is part of the "automake" utility in GNU/linux, maybe you > dont have this installed. Check if it is in your system, just type > "automake" in any console.:-) > Cheers, > > On 9/26/07, Giovanni Marco Dall'Olio wrote: >> You have to install 'aclocal-1.10'. > From Sarah.Vardy at student.griffith.edu.au Wed Sep 26 20:07:27 2007 From: Sarah.Vardy at student.griffith.edu.au (Sarah.Vardy at student.griffith.edu.au) Date: Thu, 27 Sep 2007 10:07:27 +1000 Subject: [EMBOSS] problems installing emboss In-Reply-To: <46FA774B.7070604@umdnj.edu> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> Message-ID: Hi, I've installed automake with the command yum install automake and I still get the same error I also tried the update command. Does the current package for a centos 5 linux server include aclocal-1.10? Any help would be great. Cheers, Sarah ----- Original Message ----- From: Ryan Golhar Date: Thursday, September 27, 2007 1:52 am Subject: Re: [EMBOSS] problems installing emboss Cc: emboss at lists.open-bio.org > Alternatively, you can install EMBOSS from the pre-built RPMS, > http://informatics.umdnj.edu/BioRPMs > > > Andres Pinzon wrote: > > "aclocal" is part of the "automake" utility in GNU/linux, > maybe you > > dont have this installed. Check if it is in your system, just type > > "automake" in any console.:-) > > Cheers, > > > > On 9/26/07, Giovanni Marco Dall'Olio > wrote:>> You have to install 'aclocal-1.10'. > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > Research Computing Services Sarah.Vardy at student.griffith.edu.au 0402241794 From dalloliogm at gmail.com Thu Sep 27 07:30:03 2007 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Thu, 27 Sep 2007 13:30:03 +0200 Subject: [EMBOSS] problems installing emboss In-Reply-To: References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> Message-ID: <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> ok, you are using CentOs. alternative 1: wget ftp://emboss.open-bio.org/pub/EMBOSS/contrib/RHEL/RPM/EMBOSS-5.0.0-1.i386.rpm su - rpm -i EMBOSS-5.0.0-1.i386.rpm alternative 2: yum search aclocal yum install aclocal* -> compile Emboss as you were doing before alternative 3 (smarter): read and follow the instructions to add the BioRPMs repository to your sources list: http://informatics.umdnj.edu/BioRPMs/ ; then, yum update and yum install EMBOSS I'm a debianist and I'm not used to yum and rpms.. but this should work ok. If you encounter difficulties in installing emboss using the instructions on the emboss's website, you should write to the maintainers a bug-report explaining what do you think is wrong with their page. 2007/9/27, Sarah.Vardy at student.griffith.edu.au : > Hi, > I've installed automake with the command > yum install automake > and I still get the same error > > -- ----------------------------------------------------------- My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com From dalloliogm at gmail.com Thu Sep 27 07:31:11 2007 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Thu, 27 Sep 2007 13:31:11 +0200 Subject: [EMBOSS] problems installing emboss In-Reply-To: <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> Message-ID: <5aa3b3570709270431l1f15ecb0g65e800de375ac919@mail.gmail.com> By the way, excuse-me... but why are you running emboss on a server? 2007/9/27, Giovanni Marco Dall'Olio : > : > > it's linux running centos 5 - it's a server > > > > > -- > ----------------------------------------------------------- > > My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com > -- ----------------------------------------------------------- My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com From golharam at umdnj.edu Thu Sep 27 10:41:56 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 27 Sep 2007 10:41:56 -0400 Subject: [EMBOSS] problems installing emboss In-Reply-To: <5aa3b3570709270431l1f15ecb0g65e800de375ac919@mail.gmail.com> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> <5aa3b3570709270431l1f15ecb0g65e800de375ac919@mail.gmail.com> Message-ID: <46FBC134.6040906@umdnj.edu> Perhaps for a web interface such as a EMBOSS-Explorer? We do that here to. Not all our users have accounts on our linux servers nor do they know how to use a shell Giovanni Marco Dall'Olio wrote: > By the way, excuse-me... but why are you running emboss on a server? > > > 2007/9/27, Giovanni Marco Dall'Olio : >> : >>> it's linux running centos 5 - it's a server >>> >>> >> -- >> ----------------------------------------------------------- >> >> My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com >> > > From Sarah.Vardy at student.griffith.edu.au Thu Sep 27 20:16:16 2007 From: Sarah.Vardy at student.griffith.edu.au (Sarah.Vardy at student.griffith.edu.au) Date: Fri, 28 Sep 2007 10:16:16 +1000 Subject: [EMBOSS] problems installing emboss In-Reply-To: <46FBC134.6040906@umdnj.edu> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> <5aa3b3570709270431l1f15ecb0g65e800de375ac919@mail.gmail.com> <46FBC134.6040906@umdnj.edu> Message-ID: Yep it's to run wemboss :) ----- Original Message ----- From: Ryan Golhar Date: Friday, September 28, 2007 2:31 am Subject: Re: [EMBOSS] problems installing emboss To: dalloliogm at gmail.com Cc: emboss at lists.open-bio.org > Perhaps for a web interface such as a EMBOSS-Explorer?? We > do that here > to.? Not all our users have accounts on our linux servers > nor do they > know how to use a shell > > > > Giovanni Marco Dall'Olio wrote: > > By the way, excuse-me... but why are you running emboss on a server? > > > > > > 2007/9/27, Giovanni Marco Dall'Olio : > >> : > >>> it's linux running centos 5 - it's? a server > >>> > >>> > >> -- > >> ----------------------------------------------------------- > >> > >> My Blog on Bioinformatics (italian): > http://dalloliogm.wordpress.com>> > > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > Research Computing Services Sarah.Vardy at student.griffith.edu.au 0402241794 From johnston at biochem.ucl.ac.uk Fri Sep 7 11:41:41 2007 From: johnston at biochem.ucl.ac.uk (Caroline Johnston) Date: Fri, 7 Sep 2007 12:41:41 +0100 (BST) Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c Message-ID: Hi, Trying to install the stable EMBOSS package on Ubuntu and although it configures fine make fails with the following error: gd.c: In function 'plD_init_gif_Dev': gd.c:600: error: 'png_Dev' has no member named 'palette' gd.c:601: error: 'png_Dev' has no member named 'truecolour' gd.c: In function 'plD_eop_gif': Google's being no help. Anyone know how to fix the problem? Thanks. Cass From ajb at ebi.ac.uk Fri Sep 7 14:07:57 2007 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 7 Sep 2007 15:07:57 +0100 (BST) Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c In-Reply-To: References: Message-ID: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> Hello Cass, You will get that error if the system thinks that you have a version of the GD libraries less than version 2 on your system. You would do well to check what version of GD (and its associated dev[elopment] package) you have installed. After loading any new GD package onto your system then you'll need to do the EMBOSS './configure' step again. We do not use Ubuntu here but, from memory (which could be wrong), the relevant Ubuntu packages you need will be called something like libgd2 and libgd2-dev. HTH Alan > Hi, > > Trying to install the stable EMBOSS package on Ubuntu and although it > configures fine make fails with the following error: > > gd.c: In function 'plD_init_gif_Dev': > gd.c:600: error: 'png_Dev' has no member named 'palette' > gd.c:601: error: 'png_Dev' has no member named 'truecolour' > gd.c: In function 'plD_eop_gif': > > Google's being no help. Anyone know how to fix the problem? > > Thanks. > > Cass > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From pmr at ebi.ac.uk Fri Sep 7 14:20:13 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 07 Sep 2007 15:20:13 +0100 Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c In-Reply-To: References: Message-ID: <46E15E1D.9000201@ebi.ac.uk> Caroline Johnston wrote: > Trying to install the stable EMBOSS package on Ubuntu and although it > configures fine make fails with the following error: > > gd.c: In function 'plD_init_gif_Dev': > gd.c:600: error: 'png_Dev' has no member named 'palette' > gd.c:601: error: 'png_Dev' has no member named 'truecolour' > gd.c: In function 'plD_eop_gif': What version of libgd do you have installed? We added GIF support which requires a more recent version. regards, Peter Rice From johnston at biochem.ucl.ac.uk Fri Sep 7 14:28:31 2007 From: johnston at biochem.ucl.ac.uk (Caroline Johnston) Date: Fri, 7 Sep 2007 15:28:31 +0100 (BST) Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c In-Reply-To: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> References: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> Message-ID: On Fri, 7 Sep 2007 ajb at ebi.ac.uk wrote: > You will get that error if the system thinks that you have a > version of the GD libraries less than version 2 on your system. Newer versions installed. Seems to be working grand now. Cheers, Cass xx From steffen_moeller at gmx.de Fri Sep 7 14:37:54 2007 From: steffen_moeller at gmx.de (Steffen Moeller) Date: Fri, 7 Sep 2007 16:37:54 +0200 Subject: [EMBOSS] EMBOSS Install problem: Can't make gd.c In-Reply-To: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> References: <57596.81.98.241.17.1189174077.squirrel@webmail.ebi.ac.uk> Message-ID: <200709071637.54603.steffen_moeller@gmx.de> Hello, There is a Debian package for EMBOSS 5 provided by Charles Plessy of the Debian-Med community that may be directly installable on Ubuntu, too. Please give it a try and be so kind to report. You find more details at http://wiki.debian.org/pkg-emboss. Cheers, Steffen On Friday 07 September 2007 16:07:57 ajb at ebi.ac.uk wrote: > Hello Cass, > > You will get that error if the system thinks that you have a > version of the GD libraries less than version 2 on your system. > > You would do well to check what version of GD (and its associated > dev[elopment] package) you have installed. After loading > any new GD package onto your system then you'll need to > do the EMBOSS './configure' step again. > > We do not use Ubuntu here but, from memory (which could be wrong), the > relevant Ubuntu packages you need will be called something like libgd2 and > libgd2-dev. > > HTH > > Alan > > > Hi, > > > > Trying to install the stable EMBOSS package on Ubuntu and although it > > configures fine make fails with the following error: > > > > gd.c: In function 'plD_init_gif_Dev': > > gd.c:600: error: 'png_Dev' has no member named 'palette' > > gd.c:601: error: 'png_Dev' has no member named 'truecolour' > > gd.c: In function 'plD_eop_gif': > > > > Google's being no help. Anyone know how to fix the problem? > > > > Thanks. > > > > Cass > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part. URL: From Marco.Berg-van-den at DSM.COM Fri Sep 21 11:24:02 2007 From: Marco.Berg-van-den at DSM.COM (Berg-van-den, Marco) Date: Fri, 21 Sep 2007 13:24:02 +0200 Subject: [EMBOSS] question about 'fuzznuc'and whole datases Message-ID: <944926C5F6D8DD4588FDB9307728B9365560F8@nldlf12w3ms001.CORPAD.DSM-GROUP.COM> Hi, I would like to do a pattern search against the whole GenBank or EMBL database. How do I do that within fuzznuc? Or should I use another program for that? Thanks in advance, Marco van den Berg DISCLAIMER: This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. From sufei at mail.sdu.edu.cn Fri Sep 21 13:47:09 2007 From: sufei at mail.sdu.edu.cn (=?gb2312?B?y9Xssw==?=) Date: Fri, 21 Sep 2007 21:47:09 +0800 Subject: [EMBOSS] (no subject) Message-ID: <390382598.22106@mail.sdu.edu.cn> Sorry, I am not familiar with the emboss programs. I am studying, you can ask others. Yours Tonny +++++++++++++++++++++++++++++++++++++++++++++++++++++++= Shandong University The department of life science China ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From Sarah.Vardy at student.griffith.edu.au Tue Sep 25 04:50:37 2007 From: Sarah.Vardy at student.griffith.edu.au (Sarah.Vardy at student.griffith.edu.au) Date: Tue, 25 Sep 2007 14:50:37 +1000 Subject: [EMBOSS] problems installing emboss Message-ID: Hi, I am having some problems installing emboss. When I try to 'make' the installation the error message tells me that aclocal-1.10 is missing. Can anyone tell me how I solve this error? Thank you. Sarah From dalloliogm at gmail.com Wed Sep 26 09:40:10 2007 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Wed, 26 Sep 2007 11:40:10 +0200 Subject: [EMBOSS] problems installing emboss In-Reply-To: References: Message-ID: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> You have to install 'aclocal-1.10'. Why don't you tell us which operating system are you using? Win or Linux? In the latter case, it is possible that there is already a binary package available for your distribution, so you will be able to install emboss without compiling. 2007/9/25, Sarah.Vardy at student.griffith.edu.au : > Hi, > > > > I am having some problems installing emboss. > > > > When I try to 'make' the installation the error message tells me that > aclocal-1.10 is missing. Can anyone tell me how I solve this error? > > > > Thank you. > > > > Sarah > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- ----------------------------------------------------------- My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com From dksamuel at gmail.com Wed Sep 26 10:37:24 2007 From: dksamuel at gmail.com (Duleep Samuel) Date: Wed, 26 Sep 2007 16:07:24 +0530 Subject: [EMBOSS] Fwd: problems installing emboss In-Reply-To: References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> Message-ID: If on windows XP the binary installs like a dream,Samuel On 9/26/07, Giovanni Marco Dall'Olio wrote: > > You have to install 'aclocal-1.10'. > > Why don't you tell us which operating system are you using? Win or Linux? > In the latter case, it is possible that there is already a binary > package available for your distribution, so you will be able to > install emboss without compiling. > > > > 2007/9/25, Sarah.Vardy at student.griffith.edu.au > : > > Hi, > > > > > > > > I am having some problems installing emboss. > > > > > > > > When I try to 'make' the installation the error message tells me that > > aclocal-1.10 is missing. Can anyone tell me how I solve this error? > > > > > > > > Thank you. > > > > > > > > Sarah > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > -- > ----------------------------------------------------------- > > My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From andrespinzon at gmail.com Wed Sep 26 14:54:30 2007 From: andrespinzon at gmail.com (Andres Pinzon) Date: Wed, 26 Sep 2007 09:54:30 -0500 Subject: [EMBOSS] problems installing emboss In-Reply-To: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> Message-ID: <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> "aclocal" is part of the "automake" utility in GNU/linux, maybe you dont have this installed. Check if it is in your system, just type "automake" in any console.:-) Cheers, On 9/26/07, Giovanni Marco Dall'Olio wrote: > You have to install 'aclocal-1.10'. -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From golharam at umdnj.edu Wed Sep 26 15:14:19 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 26 Sep 2007 11:14:19 -0400 Subject: [EMBOSS] problems installing emboss In-Reply-To: <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> Message-ID: <46FA774B.7070604@umdnj.edu> Alternatively, you can install EMBOSS from the pre-built RPMS, http://informatics.umdnj.edu/BioRPMs Andres Pinzon wrote: > "aclocal" is part of the "automake" utility in GNU/linux, maybe you > dont have this installed. Check if it is in your system, just type > "automake" in any console.:-) > Cheers, > > On 9/26/07, Giovanni Marco Dall'Olio wrote: >> You have to install 'aclocal-1.10'. > From Sarah.Vardy at student.griffith.edu.au Thu Sep 27 00:07:27 2007 From: Sarah.Vardy at student.griffith.edu.au (Sarah.Vardy at student.griffith.edu.au) Date: Thu, 27 Sep 2007 10:07:27 +1000 Subject: [EMBOSS] problems installing emboss In-Reply-To: <46FA774B.7070604@umdnj.edu> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> Message-ID: Hi, I've installed automake with the command yum install automake and I still get the same error I also tried the update command. Does the current package for a centos 5 linux server include aclocal-1.10? Any help would be great. Cheers, Sarah ----- Original Message ----- From: Ryan Golhar Date: Thursday, September 27, 2007 1:52 am Subject: Re: [EMBOSS] problems installing emboss Cc: emboss at lists.open-bio.org > Alternatively, you can install EMBOSS from the pre-built RPMS, > http://informatics.umdnj.edu/BioRPMs > > > Andres Pinzon wrote: > > "aclocal" is part of the "automake" utility in GNU/linux, > maybe you > > dont have this installed. Check if it is in your system, just type > > "automake" in any console.:-) > > Cheers, > > > > On 9/26/07, Giovanni Marco Dall'Olio > wrote:>> You have to install 'aclocal-1.10'. > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > Research Computing Services Sarah.Vardy at student.griffith.edu.au 0402241794 From dalloliogm at gmail.com Thu Sep 27 11:30:03 2007 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Thu, 27 Sep 2007 13:30:03 +0200 Subject: [EMBOSS] problems installing emboss In-Reply-To: References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> Message-ID: <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> ok, you are using CentOs. alternative 1: wget ftp://emboss.open-bio.org/pub/EMBOSS/contrib/RHEL/RPM/EMBOSS-5.0.0-1.i386.rpm su - rpm -i EMBOSS-5.0.0-1.i386.rpm alternative 2: yum search aclocal yum install aclocal* -> compile Emboss as you were doing before alternative 3 (smarter): read and follow the instructions to add the BioRPMs repository to your sources list: http://informatics.umdnj.edu/BioRPMs/ ; then, yum update and yum install EMBOSS I'm a debianist and I'm not used to yum and rpms.. but this should work ok. If you encounter difficulties in installing emboss using the instructions on the emboss's website, you should write to the maintainers a bug-report explaining what do you think is wrong with their page. 2007/9/27, Sarah.Vardy at student.griffith.edu.au : > Hi, > I've installed automake with the command > yum install automake > and I still get the same error > > -- ----------------------------------------------------------- My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com From dalloliogm at gmail.com Thu Sep 27 11:31:11 2007 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Thu, 27 Sep 2007 13:31:11 +0200 Subject: [EMBOSS] problems installing emboss In-Reply-To: <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> Message-ID: <5aa3b3570709270431l1f15ecb0g65e800de375ac919@mail.gmail.com> By the way, excuse-me... but why are you running emboss on a server? 2007/9/27, Giovanni Marco Dall'Olio : > : > > it's linux running centos 5 - it's a server > > > > > -- > ----------------------------------------------------------- > > My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com > -- ----------------------------------------------------------- My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com From golharam at umdnj.edu Thu Sep 27 14:41:56 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 27 Sep 2007 10:41:56 -0400 Subject: [EMBOSS] problems installing emboss In-Reply-To: <5aa3b3570709270431l1f15ecb0g65e800de375ac919@mail.gmail.com> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> <5aa3b3570709270431l1f15ecb0g65e800de375ac919@mail.gmail.com> Message-ID: <46FBC134.6040906@umdnj.edu> Perhaps for a web interface such as a EMBOSS-Explorer? We do that here to. Not all our users have accounts on our linux servers nor do they know how to use a shell Giovanni Marco Dall'Olio wrote: > By the way, excuse-me... but why are you running emboss on a server? > > > 2007/9/27, Giovanni Marco Dall'Olio : >> : >>> it's linux running centos 5 - it's a server >>> >>> >> -- >> ----------------------------------------------------------- >> >> My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com >> > > From Sarah.Vardy at student.griffith.edu.au Fri Sep 28 00:16:16 2007 From: Sarah.Vardy at student.griffith.edu.au (Sarah.Vardy at student.griffith.edu.au) Date: Fri, 28 Sep 2007 10:16:16 +1000 Subject: [EMBOSS] problems installing emboss In-Reply-To: <46FBC134.6040906@umdnj.edu> References: <5aa3b3570709260240o5aa4cd4cyeb8ce6e00b4e0b3f@mail.gmail.com> <8968fc7e0709260754pffacf95s2ad68251b33d39ab@mail.gmail.com> <46FA774B.7070604@umdnj.edu> <5aa3b3570709270430y2405e27fkac919c9aeff3b7e6@mail.gmail.com> <5aa3b3570709270431l1f15ecb0g65e800de375ac919@mail.gmail.com> <46FBC134.6040906@umdnj.edu> Message-ID: Yep it's to run wemboss :) ----- Original Message ----- From: Ryan Golhar Date: Friday, September 28, 2007 2:31 am Subject: Re: [EMBOSS] problems installing emboss To: dalloliogm at gmail.com Cc: emboss at lists.open-bio.org > Perhaps for a web interface such as a EMBOSS-Explorer?? We > do that here > to.? Not all our users have accounts on our linux servers > nor do they > know how to use a shell > > > > Giovanni Marco Dall'Olio wrote: > > By the way, excuse-me... but why are you running emboss on a server? > > > > > > 2007/9/27, Giovanni Marco Dall'Olio : > >> : > >>> it's linux running centos 5 - it's? a server > >>> > >>> > >> -- > >> ----------------------------------------------------------- > >> > >> My Blog on Bioinformatics (italian): > http://dalloliogm.wordpress.com>> > > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > Research Computing Services Sarah.Vardy at student.griffith.edu.au 0402241794