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From: Joshua O. <jo...@gm...> - 2013-10-17 00:32:00
|
Notice to all developers - I'll be migrating Ergatis to GitHub this Saturday evening. Please make sure any uncommitted code you might have out is committed to SF.net before then. I'll be happy to add active contributors to Ergatis as Collaborators in GitHub, so you can continue to make direct commits without needing to do pull requests. Let me know if you have any issues with this. Joshua |
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From: Celine N. <Cel...@to...> - 2012-03-20 16:44:18
|
Hi Ergatis team, I tried to change SGE parameters in an iterable component. But I found a problem, if I set an runDistributedCommand into an iterator component, I never get the end of the the runDistributedCommand. Have you ever seen it ? Thank Céline -- Céline Noirot Plateforme Bioinfo Genotoul- Unité BIA - INRA Toulouse 31326 Castanet-Tolosan Tel. 05 61 28 57 24 http://bioinfo.genotoul.fr |
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From: Chris H. <che...@cg...> - 2011-12-21 00:36:38
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Kevin, I committed revision 7535, which fixes this problem for our pipeline via a bugfix to bsml2fasta.pl and small addition to translate_sequence.pl. Can you please look at translate_sequence.pl in particular to make sure I haven't broken some other corner case fixing this one? bsml2fasta.pl - This script already addressed my problem by using the 'identifier' attr of 'Seq-data-import' to map to the fasta header. However a bug caused it to attempt this mapping twice - I fixed this and it works. translate_sequence.pl - I used the same method as bsml2fasta.pl does, and use the fasta identifier when it is available from the source bsml. Thanks, Chris On Fri, 16 Dec 2011, Chris Hemmerich wrote: > > Kevin, > > I ran the header > >> 1 > > through a v16 (glimmer, non-pseudo) prok pipeline, and the pipeline dies > with mapping problems between '1' and '_1' as a sequence header. Rather > than modify these sequences at the beginning, I'm looking at injecting > getCleanID where a sequence id extracted from a BSML file is mapped > against external sequence ids - which will avoid the problem of changing > headers when not necessary. > > The first two scripts to fail are bsml2fasta.pl and translate_sequence.pl. > Patching bsml2fasta.pl is straightforward, but translate_sequence.pl is > more complicated as it can take either a fasta file or bsml file as input > and then calls Fasta::SimpleIndexer to index the fasta file. My plan is to > add an optional 'use_bsml' named parameter to Fasta::SimpleIndexer::new > that causes getCleanID to be called on the header names and then modify > translate_sequence.pl to use that parameter when it detects a BSML input. > > Cheers, > Chris > > On Fri, 16 Dec 2011, Kevin Galens wrote: > >> Chris, >> >> 1. Yeah, I've thought about the mapping file as well. Although, I'd hate >> to add this functionality to a general component like BER with the only >> application for the change being the Prok Pipeline. A better solution >> would be to pre-parse the BER bsml files within the start_site_curation >> component and create the mapping file just before the analyze overlaps >> step. I'll take a look into changing this. >> >> 2. Sounds good. >> >> 3. Thanks for looking into this. >> >> On 12/15/11 3:10 PM, "Chris Hemmerich" <che...@cg...> wrote: >> >>> >>> Thanks, Kevin. Responses are below. >>> >>> On Thu, 15 Dec 2011, Kevin Galens wrote: >>> >>>> Chris, >>>> >>>> Here are some comments on the proposed changes below. >>>> >>>> 1. start_site_curation.pl >>>> >>>> Without opening the evidence bsml files, how do you determine which >>>> evidence file contains information for which polypeptide? Originally, >>>> when >>>> I wrote this script I relied on the filenames. This worked in most >>>> cases, >>>> but for some other applications (outside of the prok pipeline) this >>>> assumption did not hold true. For example, one ber bsml file might >>>> contain >>>> alignment information for multiple polypeptides. >>>> >>> >>> We read in the defined peptides from INPUT_FILE and then match on the ber >>> evidence file name, so it would break on the example above. We can >>> continue to maintain this patch for ISGA, or if the slowdown is a general >>> problem, a solution might be to accept an optional mapping file from id >>> -> >>> file, and then modify the ber component to produce such a mapping. >>> >>>> 2. overlap_analysis.pl >>>> >>>> I can't think of any issues with this. Surprised we made that required >>>> in >>>> the first place. >>>> >>> >>> Ok, if no one else objects, I'll commit this. >>> >>>> 3 & 4. bsml2fasta.pl, split_multifasta.pl >>>> >>>> This would need to be an optional parameter. I can see cases where we >>>> would not want the sequence headers to be changed when using these >>>> components. Was this causing issues within the pipeline? Or just general >>>> confusion? >>>> >>> >>> Vanilla split_multifasta.pl cleans the header to be a safe file name. But >>> if this name is different than what getCleanID() produces, the prok. >>> pipeline will break because it can not map the fasta header onto the BSML >>> entry. I'll run a test on v16 and get back to you with where the pipeline >>> fails, maybe there is a better solution than these patches. >>> >>> Thanks, >>> Chris >>> >>>> Kevin >>>> >>>> On 12/15/11 1:39 PM, "Chris Hemmerich" <che...@cg...> wrote: >>>> >>>>> >>>>> We have four modified Ergatis components (made for ISGA) that are more >>>>> than bugfixes, but I believe are safe to commit without breaking other >>>>> people's pipelines. I've listed them below, do any of them raise >>>>> objections? >>>>> >>>>> 1: start_site_curation.pl >>>>> >>>>> In trunk, this script loads every evidence file for each contig - >>>>> making >>>>> the script very slow for poorly assembled draft genomes. Our verson >>>>> only >>>>> opens evidence files for the polypeptides on a given contig. >>>>> >>>>> 2: overlap_analysis.pl >>>>> >>>>> We change the ncRNA input to be optional as we allow users to disable >>>>> the >>>>> ncRNA components. >>>>> >>>>> 3 & 4: bsml2fasta.pl, split_multifasta.pl >>>>> >>>>> We run sequence headers through BSML::BsmlElement->getCleanID() so that >>>>> headers are consistently scrubbed throughout the pipeline. >>>>> >>>>> Thanks, >>>>> Chris >>>>> >>>>> >>>>> ------------------------------------------------------------------------ >>>>> -- >>>>> ---- >>>>> 10 Tips for Better Server Consolidation >>>>> Server virtualization is being driven by many needs. >>>>> But none more important than the need to reduce IT complexity >>>>> while improving strategic productivity. Learn More! >>>>> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >>>>> _______________________________________________ >>>>> Ergatis-devel mailing list >>>>> Erg...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------- >>>> ----- >>>> 10 Tips for Better Server Consolidation >>>> Server virtualization is being driven by many needs. >>>> But none more important than the need to reduce IT complexity >>>> while improving strategic productivity. Learn More! >>>> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >>>> _______________________________________________ >>>> Ergatis-devel mailing list >>>> Erg...@li... >>>> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >>>> >>> >>> -------------------------------------------------------------------------- >>> ---- >>> 10 Tips for Better Server Consolidation >>> Server virtualization is being driven by many needs. >>> But none more important than the need to reduce IT complexity >>> while improving strategic productivity. Learn More! >>> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >>> _______________________________________________ >>> Ergatis-devel mailing list >>> Erg...@li... >>> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >> >> >> >> ------------------------------------------------------------------------------ >> Learn Windows Azure Live! Tuesday, Dec 13, 2011 >> Microsoft is holding a special Learn Windows Azure training event for >> developers. It will provide a great way to learn Windows Azure and what it >> provides. You can attend the event by watching it streamed LIVE online. >> Learn more at http://p.sf.net/sfu/ms-windowsazure >> _______________________________________________ >> Ergatis-devel mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >> > > ------------------------------------------------------------------------------ > Learn Windows Azure Live! Tuesday, Dec 13, 2011 > Microsoft is holding a special Learn Windows Azure training event for > developers. It will provide a great way to learn Windows Azure and what it > provides. You can attend the event by watching it streamed LIVE online. > Learn more at http://p.sf.net/sfu/ms-windowsazure > _______________________________________________ > Ergatis-devel mailing list > Erg...@li... > https://lists.sourceforge.net/lists/listinfo/ergatis-devel > |
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From: Chris H. <che...@cg...> - 2011-12-17 01:13:16
|
Kevin, I ran the header > 1 through a v16 (glimmer, non-pseudo) prok pipeline, and the pipeline dies with mapping problems between '1' and '_1' as a sequence header. Rather than modify these sequences at the beginning, I'm looking at injecting getCleanID where a sequence id extracted from a BSML file is mapped against external sequence ids - which will avoid the problem of changing headers when not necessary. The first two scripts to fail are bsml2fasta.pl and translate_sequence.pl. Patching bsml2fasta.pl is straightforward, but translate_sequence.pl is more complicated as it can take either a fasta file or bsml file as input and then calls Fasta::SimpleIndexer to index the fasta file. My plan is to add an optional 'use_bsml' named parameter to Fasta::SimpleIndexer::new that causes getCleanID to be called on the header names and then modify translate_sequence.pl to use that parameter when it detects a BSML input. Cheers, Chris On Fri, 16 Dec 2011, Kevin Galens wrote: > Chris, > > 1. Yeah, I've thought about the mapping file as well. Although, I'd hate > to add this functionality to a general component like BER with the only > application for the change being the Prok Pipeline. A better solution > would be to pre-parse the BER bsml files within the start_site_curation > component and create the mapping file just before the analyze overlaps > step. I'll take a look into changing this. > > 2. Sounds good. > > 3. Thanks for looking into this. > > On 12/15/11 3:10 PM, "Chris Hemmerich" <che...@cg...> wrote: > >> >> Thanks, Kevin. Responses are below. >> >> On Thu, 15 Dec 2011, Kevin Galens wrote: >> >>> Chris, >>> >>> Here are some comments on the proposed changes below. >>> >>> 1. start_site_curation.pl >>> >>> Without opening the evidence bsml files, how do you determine which >>> evidence file contains information for which polypeptide? Originally, >>> when >>> I wrote this script I relied on the filenames. This worked in most >>> cases, >>> but for some other applications (outside of the prok pipeline) this >>> assumption did not hold true. For example, one ber bsml file might >>> contain >>> alignment information for multiple polypeptides. >>> >> >> We read in the defined peptides from INPUT_FILE and then match on the ber >> evidence file name, so it would break on the example above. We can >> continue to maintain this patch for ISGA, or if the slowdown is a general >> problem, a solution might be to accept an optional mapping file from id >> -> >> file, and then modify the ber component to produce such a mapping. >> >>> 2. overlap_analysis.pl >>> >>> I can't think of any issues with this. Surprised we made that required >>> in >>> the first place. >>> >> >> Ok, if no one else objects, I'll commit this. >> >>> 3 & 4. bsml2fasta.pl, split_multifasta.pl >>> >>> This would need to be an optional parameter. I can see cases where we >>> would not want the sequence headers to be changed when using these >>> components. Was this causing issues within the pipeline? Or just general >>> confusion? >>> >> >> Vanilla split_multifasta.pl cleans the header to be a safe file name. But >> if this name is different than what getCleanID() produces, the prok. >> pipeline will break because it can not map the fasta header onto the BSML >> entry. I'll run a test on v16 and get back to you with where the pipeline >> fails, maybe there is a better solution than these patches. >> >> Thanks, >> Chris >> >>> Kevin >>> >>> On 12/15/11 1:39 PM, "Chris Hemmerich" <che...@cg...> wrote: >>> >>>> >>>> We have four modified Ergatis components (made for ISGA) that are more >>>> than bugfixes, but I believe are safe to commit without breaking other >>>> people's pipelines. I've listed them below, do any of them raise >>>> objections? >>>> >>>> 1: start_site_curation.pl >>>> >>>> In trunk, this script loads every evidence file for each contig - >>>> making >>>> the script very slow for poorly assembled draft genomes. Our verson >>>> only >>>> opens evidence files for the polypeptides on a given contig. >>>> >>>> 2: overlap_analysis.pl >>>> >>>> We change the ncRNA input to be optional as we allow users to disable >>>> the >>>> ncRNA components. >>>> >>>> 3 & 4: bsml2fasta.pl, split_multifasta.pl >>>> >>>> We run sequence headers through BSML::BsmlElement->getCleanID() so that >>>> headers are consistently scrubbed throughout the pipeline. >>>> >>>> Thanks, >>>> Chris >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> -- >>>> ---- >>>> 10 Tips for Better Server Consolidation >>>> Server virtualization is being driven by many needs. >>>> But none more important than the need to reduce IT complexity >>>> while improving strategic productivity. Learn More! >>>> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >>>> _______________________________________________ >>>> Ergatis-devel mailing list >>>> Erg...@li... >>>> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> ----- >>> 10 Tips for Better Server Consolidation >>> Server virtualization is being driven by many needs. >>> But none more important than the need to reduce IT complexity >>> while improving strategic productivity. Learn More! >>> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >>> _______________________________________________ >>> Ergatis-devel mailing list >>> Erg...@li... >>> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >>> >> >> -------------------------------------------------------------------------- >> ---- >> 10 Tips for Better Server Consolidation >> Server virtualization is being driven by many needs. >> But none more important than the need to reduce IT complexity >> while improving strategic productivity. Learn More! >> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >> _______________________________________________ >> Ergatis-devel mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-devel > > > > ------------------------------------------------------------------------------ > Learn Windows Azure Live! Tuesday, Dec 13, 2011 > Microsoft is holding a special Learn Windows Azure training event for > developers. It will provide a great way to learn Windows Azure and what it > provides. You can attend the event by watching it streamed LIVE online. > Learn more at http://p.sf.net/sfu/ms-windowsazure > _______________________________________________ > Ergatis-devel mailing list > Erg...@li... > https://lists.sourceforge.net/lists/listinfo/ergatis-devel > |
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From: Kevin G. <kev...@gm...> - 2011-12-16 14:39:29
|
Chris, 1. Yeah, I've thought about the mapping file as well. Although, I'd hate to add this functionality to a general component like BER with the only application for the change being the Prok Pipeline. A better solution would be to pre-parse the BER bsml files within the start_site_curation component and create the mapping file just before the analyze overlaps step. I'll take a look into changing this. 2. Sounds good. 3. Thanks for looking into this. On 12/15/11 3:10 PM, "Chris Hemmerich" <che...@cg...> wrote: > >Thanks, Kevin. Responses are below. > >On Thu, 15 Dec 2011, Kevin Galens wrote: > >> Chris, >> >> Here are some comments on the proposed changes below. >> >> 1. start_site_curation.pl >> >> Without opening the evidence bsml files, how do you determine which >> evidence file contains information for which polypeptide? Originally, >>when >> I wrote this script I relied on the filenames. This worked in most >>cases, >> but for some other applications (outside of the prok pipeline) this >> assumption did not hold true. For example, one ber bsml file might >>contain >> alignment information for multiple polypeptides. >> > >We read in the defined peptides from INPUT_FILE and then match on the ber >evidence file name, so it would break on the example above. We can >continue to maintain this patch for ISGA, or if the slowdown is a general >problem, a solution might be to accept an optional mapping file from id >-> >file, and then modify the ber component to produce such a mapping. > >> 2. overlap_analysis.pl >> >> I can't think of any issues with this. Surprised we made that required >>in >> the first place. >> > >Ok, if no one else objects, I'll commit this. > >> 3 & 4. bsml2fasta.pl, split_multifasta.pl >> >> This would need to be an optional parameter. I can see cases where we >> would not want the sequence headers to be changed when using these >> components. Was this causing issues within the pipeline? Or just general >> confusion? >> > >Vanilla split_multifasta.pl cleans the header to be a safe file name. But >if this name is different than what getCleanID() produces, the prok. >pipeline will break because it can not map the fasta header onto the BSML >entry. I'll run a test on v16 and get back to you with where the pipeline >fails, maybe there is a better solution than these patches. > >Thanks, > Chris > >> Kevin >> >> On 12/15/11 1:39 PM, "Chris Hemmerich" <che...@cg...> wrote: >> >>> >>> We have four modified Ergatis components (made for ISGA) that are more >>> than bugfixes, but I believe are safe to commit without breaking other >>> people's pipelines. I've listed them below, do any of them raise >>> objections? >>> >>> 1: start_site_curation.pl >>> >>> In trunk, this script loads every evidence file for each contig - >>>making >>> the script very slow for poorly assembled draft genomes. Our verson >>>only >>> opens evidence files for the polypeptides on a given contig. >>> >>> 2: overlap_analysis.pl >>> >>> We change the ncRNA input to be optional as we allow users to disable >>>the >>> ncRNA components. >>> >>> 3 & 4: bsml2fasta.pl, split_multifasta.pl >>> >>> We run sequence headers through BSML::BsmlElement->getCleanID() so that >>> headers are consistently scrubbed throughout the pipeline. >>> >>> Thanks, >>> Chris >>> >>> >>>------------------------------------------------------------------------ >>>-- >>> ---- >>> 10 Tips for Better Server Consolidation >>> Server virtualization is being driven by many needs. >>> But none more important than the need to reduce IT complexity >>> while improving strategic productivity. Learn More! >>> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >>> _______________________________________________ >>> Ergatis-devel mailing list >>> Erg...@li... >>> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >> >> >> >> >>------------------------------------------------------------------------- >>----- >> 10 Tips for Better Server Consolidation >> Server virtualization is being driven by many needs. >> But none more important than the need to reduce IT complexity >> while improving strategic productivity. Learn More! >> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >> _______________________________________________ >> Ergatis-devel mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >> > >-------------------------------------------------------------------------- >---- >10 Tips for Better Server Consolidation >Server virtualization is being driven by many needs. >But none more important than the need to reduce IT complexity >while improving strategic productivity. Learn More! >http://www.accelacomm.com/jaw/sdnl/114/51507609/ >_______________________________________________ >Ergatis-devel mailing list >Erg...@li... >https://lists.sourceforge.net/lists/listinfo/ergatis-devel |
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From: Chris H. <che...@cg...> - 2011-12-15 20:10:19
|
Thanks, Kevin. Responses are below. On Thu, 15 Dec 2011, Kevin Galens wrote: > Chris, > > Here are some comments on the proposed changes below. > > 1. start_site_curation.pl > > Without opening the evidence bsml files, how do you determine which > evidence file contains information for which polypeptide? Originally, when > I wrote this script I relied on the filenames. This worked in most cases, > but for some other applications (outside of the prok pipeline) this > assumption did not hold true. For example, one ber bsml file might contain > alignment information for multiple polypeptides. > We read in the defined peptides from INPUT_FILE and then match on the ber evidence file name, so it would break on the example above. We can continue to maintain this patch for ISGA, or if the slowdown is a general problem, a solution might be to accept an optional mapping file from id -> file, and then modify the ber component to produce such a mapping. > 2. overlap_analysis.pl > > I can't think of any issues with this. Surprised we made that required in > the first place. > Ok, if no one else objects, I'll commit this. > 3 & 4. bsml2fasta.pl, split_multifasta.pl > > This would need to be an optional parameter. I can see cases where we > would not want the sequence headers to be changed when using these > components. Was this causing issues within the pipeline? Or just general > confusion? > Vanilla split_multifasta.pl cleans the header to be a safe file name. But if this name is different than what getCleanID() produces, the prok. pipeline will break because it can not map the fasta header onto the BSML entry. I'll run a test on v16 and get back to you with where the pipeline fails, maybe there is a better solution than these patches. Thanks, Chris > Kevin > > On 12/15/11 1:39 PM, "Chris Hemmerich" <che...@cg...> wrote: > >> >> We have four modified Ergatis components (made for ISGA) that are more >> than bugfixes, but I believe are safe to commit without breaking other >> people's pipelines. I've listed them below, do any of them raise >> objections? >> >> 1: start_site_curation.pl >> >> In trunk, this script loads every evidence file for each contig - making >> the script very slow for poorly assembled draft genomes. Our verson only >> opens evidence files for the polypeptides on a given contig. >> >> 2: overlap_analysis.pl >> >> We change the ncRNA input to be optional as we allow users to disable the >> ncRNA components. >> >> 3 & 4: bsml2fasta.pl, split_multifasta.pl >> >> We run sequence headers through BSML::BsmlElement->getCleanID() so that >> headers are consistently scrubbed throughout the pipeline. >> >> Thanks, >> Chris >> >> -------------------------------------------------------------------------- >> ---- >> 10 Tips for Better Server Consolidation >> Server virtualization is being driven by many needs. >> But none more important than the need to reduce IT complexity >> while improving strategic productivity. Learn More! >> http://www.accelacomm.com/jaw/sdnl/114/51507609/ >> _______________________________________________ >> Ergatis-devel mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-devel > > > > ------------------------------------------------------------------------------ > 10 Tips for Better Server Consolidation > Server virtualization is being driven by many needs. > But none more important than the need to reduce IT complexity > while improving strategic productivity. Learn More! > http://www.accelacomm.com/jaw/sdnl/114/51507609/ > _______________________________________________ > Ergatis-devel mailing list > Erg...@li... > https://lists.sourceforge.net/lists/listinfo/ergatis-devel > |
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From: Kevin G. <kev...@gm...> - 2011-12-15 18:49:17
|
Chris, Here are some comments on the proposed changes below. 1. start_site_curation.pl Without opening the evidence bsml files, how do you determine which evidence file contains information for which polypeptide? Originally, when I wrote this script I relied on the filenames. This worked in most cases, but for some other applications (outside of the prok pipeline) this assumption did not hold true. For example, one ber bsml file might contain alignment information for multiple polypeptides. 2. overlap_analysis.pl I can't think of any issues with this. Surprised we made that required in the first place. 3 & 4. bsml2fasta.pl, split_multifasta.pl This would need to be an optional parameter. I can see cases where we would not want the sequence headers to be changed when using these components. Was this causing issues within the pipeline? Or just general confusion? Kevin On 12/15/11 1:39 PM, "Chris Hemmerich" <che...@cg...> wrote: > >We have four modified Ergatis components (made for ISGA) that are more >than bugfixes, but I believe are safe to commit without breaking other >people's pipelines. I've listed them below, do any of them raise >objections? > >1: start_site_curation.pl > >In trunk, this script loads every evidence file for each contig - making >the script very slow for poorly assembled draft genomes. Our verson only >opens evidence files for the polypeptides on a given contig. > >2: overlap_analysis.pl > >We change the ncRNA input to be optional as we allow users to disable the >ncRNA components. > >3 & 4: bsml2fasta.pl, split_multifasta.pl > >We run sequence headers through BSML::BsmlElement->getCleanID() so that >headers are consistently scrubbed throughout the pipeline. > >Thanks, > Chris > >-------------------------------------------------------------------------- >---- >10 Tips for Better Server Consolidation >Server virtualization is being driven by many needs. >But none more important than the need to reduce IT complexity >while improving strategic productivity. Learn More! >http://www.accelacomm.com/jaw/sdnl/114/51507609/ >_______________________________________________ >Ergatis-devel mailing list >Erg...@li... >https://lists.sourceforge.net/lists/listinfo/ergatis-devel |
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From: Chris H. <che...@cg...> - 2011-12-15 18:39:46
|
We have four modified Ergatis components (made for ISGA) that are more than bugfixes, but I believe are safe to commit without breaking other people's pipelines. I've listed them below, do any of them raise objections? 1: start_site_curation.pl In trunk, this script loads every evidence file for each contig - making the script very slow for poorly assembled draft genomes. Our verson only opens evidence files for the polypeptides on a given contig. 2: overlap_analysis.pl We change the ncRNA input to be optional as we allow users to disable the ncRNA components. 3 & 4: bsml2fasta.pl, split_multifasta.pl We run sequence headers through BSML::BsmlElement->getCleanID() so that headers are consistently scrubbed throughout the pipeline. Thanks, Chris |
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From: Chris H. <che...@cg...> - 2011-10-10 19:13:34
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Thanks! That will certainly work for us (it's the workaround we've been using locally). On Mon, 10 Oct 2011, Joshua Orvis wrote: > Chris - > > I just committed a fix that should support this without the need for a > wrapper. See SVN rev 7365 and see if this works for you. > > Joshua > > > > On Mon, Oct 10, 2011 at 1:42 PM, Chris Hemmerich > <che...@cg...>wrote: > >> >> Hey, >> >> The repeatmasker component currently hardcodes the '-lib' flag in the >> .i1.xml execution of repeatmasker. We need to add support for the >> '-species' (the two flags are mutually exclusive). We'd like to do this >> in a way we can submit back to svn without breaking the component for >> others. >> >> Our current plan is to write a simple perl wrapper to manage the 'lib' and >> 'species' flag and then call repeatmasker. Does this sound reasonable? Or >> is there a better way to go about it? >> >> Thanks, >> Chris >> >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure contains a >> definitive record of customers, application performance, security >> threats, fraudulent activity and more. Splunk takes this data and makes >> sense of it. Business sense. IT sense. Common sense. >> http://p.sf.net/sfu/splunk-d2dcopy1 >> _______________________________________________ >> Ergatis-devel mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-devel >> > |
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From: Joshua O. <jo...@gm...> - 2011-10-10 18:58:44
|
Chris - I just committed a fix that should support this without the need for a wrapper. See SVN rev 7365 and see if this works for you. Joshua On Mon, Oct 10, 2011 at 1:42 PM, Chris Hemmerich <che...@cg...>wrote: > > Hey, > > The repeatmasker component currently hardcodes the '-lib' flag in the > .i1.xml execution of repeatmasker. We need to add support for the > '-species' (the two flags are mutually exclusive). We'd like to do this > in a way we can submit back to svn without breaking the component for > others. > > Our current plan is to write a simple perl wrapper to manage the 'lib' and > 'species' flag and then call repeatmasker. Does this sound reasonable? Or > is there a better way to go about it? > > Thanks, > Chris > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2dcopy1 > _______________________________________________ > Ergatis-devel mailing list > Erg...@li... > https://lists.sourceforge.net/lists/listinfo/ergatis-devel > |
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From: Chris H. <che...@cg...> - 2011-10-10 18:42:23
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Hey, The repeatmasker component currently hardcodes the '-lib' flag in the .i1.xml execution of repeatmasker. We need to add support for the '-species' (the two flags are mutually exclusive). We'd like to do this in a way we can submit back to svn without breaking the component for others. Our current plan is to write a simple perl wrapper to manage the 'lib' and 'species' flag and then call repeatmasker. Does this sound reasonable? Or is there a better way to go about it? Thanks, Chris |
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From: Joshua O. <jo...@gm...> - 2011-09-20 14:22:10
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I like the revision-based directory naming idea. I think it's extremely rare that someone would want to get a previous build version of a specific revision given our conventions for naming the releases and in what goes into them. Joshua On Tue, Sep 20, 2011 at 9:18 AM, Kevin Galens <kev...@gm...> wrote: > A new release for Ergatis is scheduled later this week / early next week . > Any developers currently working on new code, bug fixes or pipeline > changes/additions that would like these to be included in the upcoming > release should commit changes soon (be sure to update the Changelog!) or let > me know if you won't be able to include your changes for this release. > > A small proposed change for the upcoming release. In the past, we've > created release folders under the 'files' section on sourceforge site for > each release. These have been separated by build number in the past > (example, we have two ergatis-v2r15 release folders: one for build 3 and one > for build 5.) I'm suggesting that we make on folder per revision and put all > builds within that folder. In this case, we'd have a folder > named ergatis-v2r15; in the folder we'd have all the builds available for > ergatis-v2r15. > > Kevin Galens > Kev...@gm... > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2dcopy1 > _______________________________________________ > Ergatis-devel mailing list > Erg...@li... > https://lists.sourceforge.net/lists/listinfo/ergatis-devel > > |
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From: Kevin G. <kev...@gm...> - 2011-09-20 14:18:22
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A new release for Ergatis is scheduled later this week / early next week . Any developers currently working on new code, bug fixes or pipeline changes/additions that would like these to be included in the upcoming release should commit changes soon (be sure to update the Changelog!) or let me know if you won't be able to include your changes for this release. A small proposed change for the upcoming release. In the past, we've created release folders under the 'files' section on sourceforge site for each release. These have been separated by build number in the past (example, we have two ergatis-v2r15 release folders: one for build 3 and one for build 5.) I'm suggesting that we make on folder per revision and put all builds within that folder. In this case, we'd have a folder named ergatis-v2r15; in the folder we'd have all the builds available for ergatis-v2r15. Kevin Galens Kev...@gm... |
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From: Galens, K. <KG...@so...> - 2011-09-20 14:14:37
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A new release for Ergatis is scheduled later this week / early next week . Any developers currently working on new code, bug fixes or pipeline changes/additions that would like these to be included in the upcoming release should commit changes soon (be sure to update the Changelog!) or let me know if you won't be able to include your changes for this release. A small proposed change for the upcoming release. In the past, we've created release folders under the 'files' section on sourceforge site for each release. These have been separated by build number in the past (example, we have two ergatis-v2r15 release folders: one for build 3 and one for build 5.) I'm suggesting that we make on folder per revision and put all builds within that folder. In this case, we'd have a folder named ergatis-v2r15; in the folder we'd have all the builds available for ergatis-v2r15. Kevin Galens Senior Bioinformatics Engineer Institute for Genome Sciences, University of Maryland Medical School kg...@so... 401.706.5811 |
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From: Kevin G. <kev...@gm...> - 2011-07-20 18:35:32
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A new release for Ergatis is scheduled later this week/ early next week. Any developers currently working on new code, bug fixes or pipeline changes/additions that would like these to be included in the upcoming release should commit changes soon (be sure to update the Changelog!) or let me know if you won't be able to include your changes for this release. This is an effort to have more regular, smaller code releases. The last release (ergatis-v2r14) was on May 3rd and I'd like to continue bi-monthly releases. A release candidate tag for Ergatis and related projects is scheduled for tomorrow. Again, let me know if you have any concerns or are working to get something checked into the repository before the release. Kevin Galens kev...@gm... |
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From: Chris H. <che...@cg...> - 2011-03-06 05:52:26
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I haven't looked at this component before, but it looks like there is a
bug on line 140. I think the code is there to check the region between the
last feature and the right end of the contig. However, $right is still set
to the start position of the last feature rather than the end of the
contig.
Can someone confirm if this is a bug or design choice? I made the
following patch to our install with picks up that peice of sequence.
+ $right = length($seqs->{$mol}->{'residues'})-1;
if( ($right - $left) >= $length_cutoff ) {
Thanks,
Chris
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From: Joshua O. <jo...@gm...> - 2011-02-24 16:18:03
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Chris - These are good suggestions, and I've incorporated them into SVN revisions 6812 and 6813. There is now a new configuration option [grid]:sge_qsub in the ergatis.ini file. Joshua On Wed, Feb 23, 2011 at 11:55 PM, Chris Hemmerich <che...@cg...>wrote: > > I've been playing with this today and it is a great feature for us where > ergatis is running on a different OS than our compute nodes. > > I ran across two things I had to hack around to get it to run at our site. > If > you can help me come up with good solutions, I'm happy to implement and > commit > them. > > 1) qsub is not being called with a full path. Can the full path be pieced > together from existing configuration information? Or should it be a new > ergatis.config entry? > > 2) A working directory isn't passed to qsub so our home directory was > being flooded with logs and tmp files. I just changed the call in > Pipeline.pm to use the created $run_dir, but I'm not sure this is a > good or universal solution. > > $runprefix = "qsub -wd $run_dir "; > > Thanks, > Chris > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > Ergatis-devel mailing list > Erg...@li... > https://lists.sourceforge.net/lists/listinfo/ergatis-devel > |
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From: Chris H. <che...@cg...> - 2011-02-24 05:55:26
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I've been playing with this today and it is a great feature for us where
ergatis is running on a different OS than our compute nodes.
I ran across two things I had to hack around to get it to run at our site. If
you can help me come up with good solutions, I'm happy to implement and commit
them.
1) qsub is not being called with a full path. Can the full path be pieced
together from existing configuration information? Or should it be a new
ergatis.config entry?
2) A working directory isn't passed to qsub so our home directory was
being flooded with logs and tmp files. I just changed the call in
Pipeline.pm to use the created $run_dir, but I'm not sure this is a
good or universal solution.
$runprefix = "qsub -wd $run_dir ";
Thanks,
Chris
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From: Dave C. <cle...@ne...> - 2011-02-02 06:21:50
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Hello all, Yesterday, we opened registration for the March 2011 GMOD Meeting (see http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting). *That meeting is part of a larger event, GMOD Americas 2011, that also includes several Satellite Meetings on March 7*, the day after the meeting ends. Satellite meetings are smaller groups of people meeting to discuss a common interest, or work on a common problem (think special interest groups / birds-of-a-feather). Unlike the GMOD Meeting, there is *no registration fee * for the Satellites, and you don't even need to go to any other GMOD Americas events to participate in the Satellites. *If you are in the area, or attending other GMOD Americas events, or are just very interested in the topic, we strongly encourage you to attend.* The current list of Satellites (see http://gmod.oicr.on.ca/wiki/Satellite_Meetings_-_GMOD_Americas_2011) includes: - *GMOD Evo Hackathon Followup*<http://gmod.oicr.on.ca/wiki/GMOD_Evo_Hackathon#March_2011_Satellite>, organized by Duke Leto <http://gmod.oicr.on.ca/wiki/User:Dukeleto>. A followup to the GMOD Evo Hackathon<http://gmod.oicr.on.ca/wiki/GMOD_Evo_Hackathon>held at NESCent in November 2011. You didn't to participate in the original event to participate in this followup. Also, if there is interest, this satellite can extend for more than one day. - *Customizing and Extending JBrowse<http://gmod.oicr.on.ca/wiki/JBrowse> *, organized by Mitch Skinner<http://gmod.oicr.on.ca/wiki/User:MitchSkinner> . JBrowse <http://gmod.oicr.on.ca/wiki/JBrowse> has a few different extension points, but they're not (yet) well-documented or widely used. The GMOD meeting would be a good time to review those APIs<http://gmod.oicr.on.ca/wiki/Glossary#API>, relate them to the things that people want to do with them, discuss any potential changes or new APIs to support specific use cases, and potentially start to implement an extension. - *GMOD Web services toolkit* <http://gmod.oicr.on.ca/wiki/GMOD_RPC_API>, organized by Josh Goodman <http://gmod.oicr.on.ca/wiki/User:Jogoodma>. Come to work on or discuss the GMOD Web services API and the toolkit<http://gmod.oicr.on.ca/wiki/GMOD_RPC_API> . - *GMOD in the Sequencing Center*<http://gmod.oicr.on.ca/wiki/GMOD_in_the_Sequencing_Center>, organized by Chris Hemmerich <http://gmod.oicr.on.ca/wiki/User:Chemmeri>, Dave Clements <http://gmod.oicr.on.ca/wiki/User:Clements>. Sequencing centers have tremendous bioinformatics needs that GMOD can help address. Attend this satellite to find out what other sequencing centers are doing with GMOD, and how GMOD can help you help your researchers. If you are interested in participating in these, please contact the organizers, and/or add your name to the satellite's participants list on the wiki. Satellites can be organized by anyone. If you have a topic you would like to cover, please add it to the list and announce it the appropriate mailing lists. Several previous satellites are written up on the GMOD wiki, if you want an idea of what happens at a satellite. Finally, please let me and Scott know if you have any questions. Thanks, and hope to see you in March! Dave C. -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://usegalaxy.org/ |
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From: Dave C. G. H. D. <he...@gm...> - 2011-01-02 18:34:18
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Hello all, The application deadline for the 2011 GMOD Spring Training (http://gmod.org/wiki/2011_GMOD_Spring_Training) is the end of this coming Friday, January 7. Admission is competitive, so please apply by Friday to avoid being automatically placed on the waiting list. Details are below. Thanks, and happy new year! Dave C ------- Applications are now being accepted for the 2011 GMOD Spring Training course (http://gmod.org/wiki/2011_GMOD_Spring_Training), a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD components. The course will be held March 8-12 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as part of GMOD Americas 2011. These components will be covered: * Apollo - genome annotation editor * Chado - biological database schema * Galaxy - analysis and data integration framework * GBrowse - genome viewer * GBrowse_syn - synteny viewer * GFF3 - genome annotation file format and tools * InterMine - biological data mining system * JBrowse - next generation genome browser * MAKER - genome annotation pipeline * Tripal - web front end to Chado databases The deadline for applying is the end of Friday, January 7, 2011. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2010 school had over 60 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $265 (only $53 per day!). There will be a limited number of scholarships available. This may be the only GMOD School offered in 2011. If you are interested, you are strongly encouraged to apply by January 7. Links: http://gmod.org/wiki/2011_GMOD_Spring_Training http://gmod.org/wiki/GMOD_Americas_2011 http://www.nescent.org/ |
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From: Dave C. G. H. D. <he...@gm...> - 2010-12-04 00:43:29
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Applications are now being accepted for the 2011 GMOD Spring Training course a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD components. The course will be held March 8-12 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as part of GMOD Americas 2011. Links: * http://gmod.org/wiki/2011_GMOD_Spring_Training * http://gmod.org/wiki/GMOD_Americas_2011 * http://www.nescent.org/ These components will be covered: * Apollo - genome annotation editor * Chado - biological database schema * Galaxy - workflow system * GBrowse - genome viewer * GBrowse_syn - synteny viewer * GFF3 - genome annotation file format and tools * InterMine - biological data mining system * JBrowse - next generation genome browser * MAKER - genome annotation pipeline * Tripal - web front end to Chado databases The deadline for applying is the end of Friday, January 7, 2011. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2010 school had over 60 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $265 (only $53 per day!). There will be a limited number of scholarships available. This may be the only GMOD School offered in 2011. If you are interested, you are strongly encouraged to apply by January 7. Thanks, Dave Clements -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Help_Desk_Feedback |
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From: Dave C. G. H. D. <he...@gm...> - 2010-09-07 18:29:33
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Hello all, GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts on Monday, 13 September, less than a week from now. This event runs for 4 days and includes: * September 2010 GMOD Meeting - has openings * GMOD Satellite Meetings - has openings * InterMine Workshop - has openings * BioMart Workshop - full (but you can get on the short waiting list) If you haven't already registered, please do so as soon as possible. This will assure you a seat and help us plan meeting logistics. See http://gmod.org/wiki/GMOD_Europe_2010 for details and a registration link. This is the last broadcast reminder I'll send out. Please let me know if you have any questions. Thanks, Dave C. -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://hinv.jp/biocuration2010/ http://gmod.org/wiki/Help_Desk_Feedback |
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From: Dave C. G. H. D. <he...@gm...> - 2010-08-25 20:54:54
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Hello all, GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts in less than two weeks. If you are planning on attending and haven't yet registered, then please do so in the next few days. The BioMart Workshop has only a few slots left, and the registration fee for the GMOD Meeting goes from £50 to £65 on 6 September. We are encouraging people to submit topic suggestions for the GMOD Meeting and the GMOD Satellite Meetings. We are also pleased to announce that Jason Swedlow of the University of Dundee will be the guest speaker at the GMOD Meeting. Jason will speak on "The Open Microscopy Environment: Open Informatics for Biological Imaging," a particularly timely topic as many researchers move into image intensive areas such as phenotypes and gene expression, and as high-throughput imaging platforms become available. There is still space available at all 4 events, and registration for the GMOD Satellite Meetings, InterMine Workshop and BioMart Workshop is free. Scott Cain and Dave Clements Links: http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/September_2010_GMOD_Meeting http://gmod.org/wiki/Satellite_Meetings_-_GMOD_Europe_2010 http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010 http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010 |
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From: Dave C. G. H. D. <he...@gm...> - 2010-08-05 04:30:13
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GMOD Europe 2010 ================ 13-16 September 2010 Cambridge, UK http://gmod.org/wiki/GMOD_Europe_2010 We are pleased to announce GMOD Europe 2010, four days of GMOD events being held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes: 1) GMOD Community Meeting, Monday & Tuesday: Project updates, developer and user presentations and best practices, project direction. 2) GMOD Satellite Meetings, Wednesday: Special interest groups where GMOD community members meet to discuss specific topics of interest. 3) InterMine Workshop, Wednesday: A one day workshop on installing, configuring and using the InterMine biological data warehouse system. 4) BioMart Workshop, Thursday: A one day workshop on using the BioMart biological data warehouse system, including accessing data through APIs. Registration is now open for these events. There is a £50 registration fee for the GMOD Meeting to cover catered lunches, coffee/tee breaks, and other expenses. Registration for all other events is free, but still required, as space is limited. These events are open to all: GMOD users, developers, prospective users, biologists, and computer scientists. For an idea of what goes on at GMOD meetings, see http://gmod.org/wiki/January_2010_GMOD_Meeting. See you in Cambridge! Scott Cain and Dave Clements PS: If you have topics you want to have covered (or you want to cover) at the GMOD Meeting, or at the Satellite Meetings, please add them to the wiki pages, or contact us. We are also asking for guest speaker nominations for the meeting. -- http://gmod.org/wiki/GMOD_News <http://gmod.org/wiki/GMOD_News>http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback |
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From: Dave C. <cle...@ne...> - 2010-08-03 17:31:08
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Hello all, This is just a reminder to send any comments on ISGA in the next three days. Thanks, Dave C On Thu, Jul 29, 2010 at 11:07 AM, Dave Clements, GMOD Help Desk < he...@gm...> wrote: > Hello all, > > I would like to nominate ISGA for membership in GMOD. ISGA is a > bioinformatics pipeline service based on the Ergatis workflow system. ISGA > comes with prokaryotic annotation and assembly pipelines and offers an > intuitive interface for biologists to run and customize pipelines. ISGA also > integrates tools such as GBrowse and BLAST for visualizing and analyzing > pipeline results. Since ISGA utilizes Ergatis, ISGA pipelines can be > submitted back to the Ergatis community and Ergatis pipelines can be adapted > to use ISGA. > > ISGA (pronounced "I-S-G-A") was created at Indiana University's Center for > Genomics and Bioinformatics (CGB) by Chris Hemmerich, Aaron Buechlein, Ram > Podicheti, Kashi Revanna, and Qunfeng Dong. CGB also hosts a public > installation of ISGA (see Links below). > > I believe that ISGA meets all of GMOD's membership requirements (see > http://gmod.org/wiki/GMOD_Membership#Requirements). The CGB is willing to > support ISGA for at least 2 years. > > ISGA could be useful to anyone working with complex pipelines and is > directly applicable to existing and potential Ergatis users. This > nomination is going to the Ergatis and DIYA lists, and to the developers > of other GMOD components related to computational pipelines. If you have > any feedback or comments on ISGA becoming a part of GMOD, please respond > on list or send mail directly to the help desk, by the end of August 6. > > Thanks, > > Dave C > > ISGA Home Page, Tutorials, and FAQ > http://isga.cgb.indiana.edu/ > http://isga.cgb.indiana.edu/Help/Tutorial > http://isga.cgb.indiana.edu/Help/FAQ > Paper > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/8/1122 > Posters/Presentations > http://gmod.org/wiki/Image:NGSTranscriptomeISGAErgatis.pdf > http://gmod.org/wiki/Image:ISGAISMB2010Poster.pdf > http://gmod.org/wiki/Image:Jan2010ErgatisForBiologists.pdf > Ergatis > http://gmod.org/wiki/Ergatis > http://ergatis.sourceforge.net/ > GMOD Membership Requirements > http://gmod.org/wiki/GMOD_Membership#Requirements > > > -- > ===> PLEASE KEEP RESPONSES ON THE LIST <=== > http://gmod.org/wiki/GMOD_News > http://gmod.org/wiki/GMOD_Europe_2010 > http://gmod.org/wiki/Help_Desk_Feedback > > > > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > > _______________________________________________ > Diyg-pub-l mailing list > Diy...@li... > https://lists.sourceforge.net/lists/listinfo/diyg-pub-l > > -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/Help_Desk_Feedback |
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