Thread: Re: [Soaplab-users] seqretall, seqretallfeat and seqretset
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From: Sebastien M. <Seb...@un...> - 2008-10-22 12:27:48
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Idem for seqrettype ! > P.S.: seqretallfeat is already disabled ! > > > Hello, > > It seems that these three software are not available by default in EMBOSS: > cf. src/ChangeLog > (Since) Version 2.3.0 > > Seqretall, seqretallfeat and seqretset moved to 'make check'. > Seqret has all the functionality of the above. > > > You need to make a 'make check' then to copy manually these programs to > your PATH because 'make install' does not seem to do this. > > > So, ACD files for them are with the other ACD files. > I mean that they become available via soaplab. > But they cannot be run by default. > > It fails for me locally and it is the same from > http://www.ebi.ac.uk/soaplab/ > > > So, should these three programs be disabled in the xmls/emboss.xml file ? > Else you should add a remark in the Soaplab documentation > (EmbossNotes.html). > > Best regards > -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
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From: Sebastien M. <Seb...@un...> - 2008-10-22 12:28:05
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P.S.: seqretallfeat is already disabled !
Hello,
It seems that these three software are not available by default in EMBOSS:
cf. src/ChangeLog
(Since) Version 2.3.0
Seqretall, seqretallfeat and seqretset moved to 'make check'.
Seqret has all the functionality of the above.
You need to make a 'make check' then to copy manually these programs to
your PATH because 'make install' does not seem to do this.
So, ACD files for them are with the other ACD files.
I mean that they become available via soaplab.
But they cannot be run by default.
It fails for me locally and it is the same from
http://www.ebi.ac.uk/soaplab/
So, should these three programs be disabled in the xmls/emboss.xml file ?
Else you should add a remark in the Soaplab documentation
(EmbossNotes.html).
Best regards
--
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/ http://myhits.vital-it.ch/
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From: Sebastien M. <Seb...@un...> - 2008-10-22 12:28:08
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Hello,
It seems that these three software are not available by default in EMBOSS:
cf. src/ChangeLog
(Since) Version 2.3.0
Seqretall, seqretallfeat and seqretset moved to 'make check'.
Seqret has all the functionality of the above.
You need to make a 'make check' then to copy manually these programs to
your PATH because 'make install' does not seem to do this.
So, ACD files for them are with the other ACD files.
I mean that they become available via soaplab.
But they cannot be run by default.
It fails for me locally and it is the same from
http://www.ebi.ac.uk/soaplab/
So, should these three programs be disabled in the xmls/emboss.xml file ?
Else you should add a remark in the Soaplab documentation
(EmbossNotes.html).
Best regards
--
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/ http://myhits.vital-it.ch/
|
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From: Sebastien M. <Seb...@un...> - 2008-10-22 14:05:09
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Also idem for complex > Idem for seqrettype ! > > >> P.S.: seqretallfeat is already disabled ! >> >> >> Hello, >> >> It seems that these three software are not available by default in >> EMBOSS: >> cf. src/ChangeLog >> (Since) Version 2.3.0 >> >> Seqretall, seqretallfeat and seqretset moved to 'make check'. >> Seqret has all the functionality of the above. >> >> >> You need to make a 'make check' then to copy manually these programs to >> your PATH because 'make install' does not seem to do this. >> >> >> So, ACD files for them are with the other ACD files. >> I mean that they become available via soaplab. >> But they cannot be run by default. >> >> It fails for me locally and it is the same from >> http://www.ebi.ac.uk/soaplab/ >> >> >> So, should these three programs be disabled in the xmls/emboss.xml file ? >> Else you should add a remark in the Soaplab documentation >> (EmbossNotes.html). >> >> Best regards -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
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From: Mahmut U. <ul...@eb...> - 2008-10-22 14:59:57
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Hi Sebastien, Thank you for pointing these errors in Soaplab and the EBI Soplab server. I have disabled the 'seqretall', 'seqretset', 'seqrettype' and 'complex' programs in Soaplab CVS version and in the EBI Soaplab server. Current acd2xml routine gets the EMBOSS programs list from $emboss_home/share/EMBOSS/acd directory, an alternative is to use the EMBOSS wossname program. I made a note to check why EMBOSS copies these ACD files by default. Regards, Mahmut On Wed, 2008-10-22 at 16:04 +0200, Sebastien Moretti wrote: > Also idem for complex > > > Idem for seqrettype ! > > > > > >> P.S.: seqretallfeat is already disabled ! > >> > >> > >> Hello, > >> > >> It seems that these three software are not available by default |
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From: Sebastien M. <Seb...@un...> - 2008-10-22 14:53:04
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+ prima (replaced by eprimer3 ?) > Also idem for complex > >> Idem for seqrettype ! >> >> >>> P.S.: seqretallfeat is already disabled ! >>> >>> >>> Hello, >>> >>> It seems that these three software are not available by default in >>> EMBOSS: >>> cf. src/ChangeLog >>> (Since) Version 2.3.0 >>> >>> Seqretall, seqretallfeat and seqretset moved to 'make check'. >>> Seqret has all the functionality of the above. >>> >>> >>> You need to make a 'make check' then to copy manually these programs to >>> your PATH because 'make install' does not seem to do this. >>> >>> >>> So, ACD files for them are with the other ACD files. >>> I mean that they become available via soaplab. >>> But they cannot be run by default. >>> >>> It fails for me locally and it is the same from >>> http://www.ebi.ac.uk/soaplab/ >>> >>> >>> So, should these three programs be disabled in the xmls/emboss.xml >>> file ? >>> Else you should add a remark in the Soaplab documentation >>> (EmbossNotes.html). >>> >>> Best regards -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
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From: Sebastien M. <Seb...@un...> - 2008-10-22 14:54:57
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+ primers (replaced by eprimer3 !) > + prima (replaced by eprimer3 ?) > >> Also idem for complex >> >>> Idem for seqrettype ! >>> >>> >>>> P.S.: seqretallfeat is already disabled ! >>>> >>>> >>>> Hello, >>>> >>>> It seems that these three software are not available by default in >>>> EMBOSS: >>>> cf. src/ChangeLog >>>> (Since) Version 2.3.0 >>>> >>>> Seqretall, seqretallfeat and seqretset moved to 'make check'. >>>> Seqret has all the functionality of the above. >>>> >>>> >>>> You need to make a 'make check' then to copy manually these programs to >>>> your PATH because 'make install' does not seem to do this. >>>> >>>> >>>> So, ACD files for them are with the other ACD files. >>>> I mean that they become available via soaplab. >>>> But they cannot be run by default. >>>> >>>> It fails for me locally and it is the same from >>>> http://www.ebi.ac.uk/soaplab/ >>>> >>>> >>>> So, should these three programs be disabled in the xmls/emboss.xml >>>> file ? >>>> Else you should add a remark in the Soaplab documentation >>>> (EmbossNotes.html). >>>> >>>> Best regards -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
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From: Mahmut U. <ul...@eb...> - 2008-10-22 16:24:14
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> primers (replaced by eprimer3 !) > > > + prima (replaced by eprimer3 ?) It looks like, they were even not in EMBOSS-2.8. I have disabled these two applications in Soaplab and in the EBI server as well. Mahmut |
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From: Sebastien M. <Seb...@un...> - 2008-10-23 08:53:47
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>> primers (replaced by eprimer3 !) >> >>> + prima (replaced by eprimer3 ?) > > It looks like, they were even not in EMBOSS-2.8. > > I have disabled these two applications in Soaplab and in the EBI server > as well. > > Mahmut Thanks Mahmut It seems that primers and prima are always enabled. There is no update for them via CVS. And it seems there is an ACD to XML problem for the density application. The web service uses -graph as attribute but this one doesn't exist. It should be qgraph or dgraph depending on selection for quad or dual attributes. And by default, density doesn't create graph output. quad and/or dual have to be used. Is it a soaplab known problem ? Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
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From: Mahmut U. <ul...@eb...> - 2008-10-23 10:55:34
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> It seems that primers and prima are always enabled. > There is no update for them via CVS. I forgot to check in the updated emboss.xml file but it is now in CVS. > And it seems there is an ACD to XML problem for the density application. > The web service uses -graph as attribute but this one doesn't exist. > It should be qgraph or dgraph depending on selection for quad or dual > attributes. > > And by default, density doesn't create graph output. > quad and/or dual have to be used. > > Is it a soaplab known problem ? Yes. A problem dictated by the current acd2xml parser which assumes only one graphics output named 'graph'. Alan's updated density.acd and density.c files fixed the above problem in my local Soaplab installation. Regards, Mahmut |
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From: Sebastien M. <Seb...@un...> - 2008-10-23 12:49:33
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>> It seems that primers and prima are always enabled. >> There is no update for them via CVS. > > I forgot to check in the updated emboss.xml file but it is now in CVS. It seems to be the same case for newcoils, giep (replaced by iep) applications too. ACD files available but not in the PATH by default. And maybe jaspextract should be hidden because it is used to build the data for jaspscan. >> And it seems there is an ACD to XML problem for the density application. >> The web service uses -graph as attribute but this one doesn't exist. >> It should be qgraph or dgraph depending on selection for quad or dual >> attributes. >> >> And by default, density doesn't create graph output. >> quad and/or dual have to be used. >> >> Is it a soaplab known problem ? > > Yes. A problem dictated by the current acd2xml parser which assumes only > one graphics output named 'graph'. Alan's updated density.acd and > density.c files fixed the above problem in my local Soaplab > installation. I will update this files too. Thanks > Regards, > Mahmut Best regards, Sébastien -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
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From: Mahmut U. <ul...@eb...> - 2008-10-23 14:44:42
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> It seems to be the same case for newcoils, giep (replaced by iep) > applications too. > ACD files available but not in the PATH by default. > > And maybe jaspextract should be hidden because it is used to build the > data for jaspscan. Thanks. These 3 applications have also been disabled. It seems that for emboss we should use the wossname with -gui option to get the list of programs. Mahmut |
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