From kayttotuki at vtt.fi Mon Mar 1 07:30:01 2004 From: kayttotuki at vtt.fi (kayttotuki at vtt.fi) Date: Mon, 1 Mar 2004 14:30:01 +0200 (EET) Subject: [#ID:71275#] Re: Hi In-Reply-To: <200403011227.i21CR64v028583@mailgw.vtt.fi> Message-ID: <8906478.1078144201469.JavaMail.SYSTEM@espsr05> Kiitos. Viestisi on tallennettu ty?nhallintaj?rjestelm??mme. From henrikki.almusa at helsinki.fi Wed Mar 10 02:44:56 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 10 Mar 2004 09:44:56 +0200 Subject: New report format needed? Message-ID: <200403100944.56862.henrikki.almusa@helsinki.fi> Hello, There are few programs in Emboss package that create a report on sequence and its "statistics". For example are pepstat, cai, cusp and geecee. Now each of these have nearly similar formats, but not same. Basicly it would be good, if these were same and also have the header and tail sections as report format has. Format could be simple. Either rows like this # [Calculated type]: [value] or ValueType1 ValueType2 ValueType3 ... ListType1 ListType2 ListType3 : Also I wondered if it would a good idea to combine some of these programs? Since some of these calculate only one value. -- Henrikki Almusa From pmr at ebi.ac.uk Wed Mar 10 04:11:12 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 10 Mar 2004 09:11:12 +0000 Subject: New report format needed? In-Reply-To: <200403100944.56862.henrikki.almusa@helsinki.fi> References: <200403100944.56862.henrikki.almusa@helsinki.fi> Message-ID: <404EDBB0.2070804@ebi.ac.uk> Henrikki Almusa wrote: > There are few programs in Emboss package that create a report on sequence and > its "statistics". For example are pepstat, cai, cusp and geecee. Now each of > these have nearly similar formats, but not same. Basicly it would be good, if > these were same and also have the header and tail sections as report format > has. > > Format could be simple. Either rows like this > > # [Calculated type]: [value] > > or > > ValueType1 ValueType2 ValueType3 ... > ListType1 > ListType2 > ListType3 Yes ... I plan to add this very soon. The plan is like this: Add a new output ACD type "outdata" Replace "outfile" with "outdata" and define (as for report) the values Provide several output formats (includnig some kind of XML) but default to text close to the original output A complication: some programs produce several outputs like this in one text file. For these, I plan to define "outdata" once for each section, with a default of appending to the original outdata file - but the possibility to write to another file is you want to save each section separately. > Also I wondered if it would a good idea to combine some of these programs? > Since some of these calculate only one value. We can investigate that. I feel that this will mean multiple outdata definitions and may be more confusing in most cases. Thanks for the suggestion Peter From khoueiry at ibsm.cnrs-mrs.fr Thu Mar 11 10:13:14 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Thu, 11 Mar 2004 16:13:14 +0100 Subject: uninstall Emboss Message-ID: <4050820A.1020803@ibsm.cnrs-mrs.fr> Hi, I want ot know the best way to uninstall Emboss from my Linux/Debian machine. In fact i install it using the tarball. any suggesting thanks in advance -- --------------------------------- Pierre Khoueiry khoueiry at ibsm.cnrs-mrs.fr LCB - CNRS 31, Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France --------------------------------- From ableasby at hgmp.mrc.ac.uk Thu Mar 11 13:24:47 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 11 Mar 2004 18:24:47 GMT Subject: uninstall Emboss Message-ID: <200403111824.i2BIOlNo018415@bromine.hgmp.mrc.ac.uk> If you installed from /blah/EMBOSS-2.8.0 and installed to /usr/local/emboss then just: rm -rf /blah/EMBOSS-2.8.0 /usr/local/emboss If, however, you installed to just /usr/local then you may have to delete /usr/local/share/EMBOSS, then libajax + libplplot +libnucleus from /usr/local/lib and then all the emboss applications from /usr/local/bin individually. HTH Alan Bleasby RFCGR From postmaster at icsw.org.uk Mon Mar 22 07:45:55 2004 From: postmaster at icsw.org.uk (postmaster at icsw.org.uk) Date: Mon, 22 Mar 2004 12:45:55 +0000 Subject: Delivery Status Notification (Failure) Message-ID: <9zG5JRj3q000000cb@icswsbs2k3.ICSW.local> A message filter removed the following attachment(s) from this message: websites03_icsw.pif -------------- next part -------------- This is an automatically generated Delivery Status Notification. Delivery to the following recipients failed. test3 at icsw.org.uk -------------- next part -------------- An embedded message was scrubbed... From: Subject: hi Date: Mon, 22 Mar 2004 12:45:48 -0000 Size: 1102 Url: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040322/c80ca406/attachment.mht From kayttotuki at vtt.fi Mon Mar 1 12:30:01 2004 From: kayttotuki at vtt.fi (kayttotuki at vtt.fi) Date: Mon, 1 Mar 2004 14:30:01 +0200 (EET) Subject: [#ID:71275#] Re: Hi In-Reply-To: <200403011227.i21CR64v028583@mailgw.vtt.fi> Message-ID: <8906478.1078144201469.JavaMail.SYSTEM@espsr05> Kiitos. Viestisi on tallennettu ty?nhallintaj?rjestelm??mme. From henrikki.almusa at helsinki.fi Wed Mar 10 07:44:56 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 10 Mar 2004 09:44:56 +0200 Subject: New report format needed? Message-ID: <200403100944.56862.henrikki.almusa@helsinki.fi> Hello, There are few programs in Emboss package that create a report on sequence and its "statistics". For example are pepstat, cai, cusp and geecee. Now each of these have nearly similar formats, but not same. Basicly it would be good, if these were same and also have the header and tail sections as report format has. Format could be simple. Either rows like this # [Calculated type]: [value] or ValueType1 ValueType2 ValueType3 ... ListType1 ListType2 ListType3 : Also I wondered if it would a good idea to combine some of these programs? Since some of these calculate only one value. -- Henrikki Almusa From pmr at ebi.ac.uk Wed Mar 10 09:11:12 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 10 Mar 2004 09:11:12 +0000 Subject: New report format needed? In-Reply-To: <200403100944.56862.henrikki.almusa@helsinki.fi> References: <200403100944.56862.henrikki.almusa@helsinki.fi> Message-ID: <404EDBB0.2070804@ebi.ac.uk> Henrikki Almusa wrote: > There are few programs in Emboss package that create a report on sequence and > its "statistics". For example are pepstat, cai, cusp and geecee. Now each of > these have nearly similar formats, but not same. Basicly it would be good, if > these were same and also have the header and tail sections as report format > has. > > Format could be simple. Either rows like this > > # [Calculated type]: [value] > > or > > ValueType1 ValueType2 ValueType3 ... > ListType1 > ListType2 > ListType3 Yes ... I plan to add this very soon. The plan is like this: Add a new output ACD type "outdata" Replace "outfile" with "outdata" and define (as for report) the values Provide several output formats (includnig some kind of XML) but default to text close to the original output A complication: some programs produce several outputs like this in one text file. For these, I plan to define "outdata" once for each section, with a default of appending to the original outdata file - but the possibility to write to another file is you want to save each section separately. > Also I wondered if it would a good idea to combine some of these programs? > Since some of these calculate only one value. We can investigate that. I feel that this will mean multiple outdata definitions and may be more confusing in most cases. Thanks for the suggestion Peter From khoueiry at ibsm.cnrs-mrs.fr Thu Mar 11 15:13:14 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Thu, 11 Mar 2004 16:13:14 +0100 Subject: uninstall Emboss Message-ID: <4050820A.1020803@ibsm.cnrs-mrs.fr> Hi, I want ot know the best way to uninstall Emboss from my Linux/Debian machine. In fact i install it using the tarball. any suggesting thanks in advance -- --------------------------------- Pierre Khoueiry khoueiry at ibsm.cnrs-mrs.fr LCB - CNRS 31, Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France --------------------------------- From ableasby at hgmp.mrc.ac.uk Thu Mar 11 18:24:47 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 11 Mar 2004 18:24:47 GMT Subject: uninstall Emboss Message-ID: <200403111824.i2BIOlNo018415@bromine.hgmp.mrc.ac.uk> If you installed from /blah/EMBOSS-2.8.0 and installed to /usr/local/emboss then just: rm -rf /blah/EMBOSS-2.8.0 /usr/local/emboss If, however, you installed to just /usr/local then you may have to delete /usr/local/share/EMBOSS, then libajax + libplplot +libnucleus from /usr/local/lib and then all the emboss applications from /usr/local/bin individually. HTH Alan Bleasby RFCGR From postmaster at icsw.org.uk Mon Mar 22 12:45:55 2004 From: postmaster at icsw.org.uk (postmaster at icsw.org.uk) Date: Mon, 22 Mar 2004 12:45:55 +0000 Subject: Delivery Status Notification (Failure) Message-ID: <9zG5JRj3q000000cb@icswsbs2k3.ICSW.local> A message filter removed the following attachment(s) from this message: websites03_icsw.pif -------------- next part -------------- This is an automatically generated Delivery Status Notification. Delivery to the following recipients failed. test3 at icsw.org.uk -------------- next part -------------- An embedded message was scrubbed... From: Subject: hi Date: Mon, 22 Mar 2004 12:45:48 -0000 Size: 1102 URL: