# HG changeset patch # User iracooke # Date 1427414670 14400 # Node ID 6c751c59ce1868df8ebc3019d22d4cc044f4d617 # Parent 32365fec702c6f1aa0a0ccffaaa7c45762f23f10 Docker support and update for protk 1.4 diff -r 32365fec702c -r 6c751c59ce18 README --- a/README Thu Jun 26 11:39:21 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -This package is a galaxy wrapper for the MSGF+ search tool. - -Requirements: -This package uses protk, msgfplus and proteowizard, which must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file diff -r 32365fec702c -r 6c751c59ce18 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Mar 26 20:04:30 2015 -0400 @@ -0,0 +1,43 @@ +MS-GF+ +====== + +Galaxy wrapper for the `MS-GF+`__ tandem ms search tool + +.. _msgfplus: http://proteomics.ucsd.edu/software-tools/ms-gf/ +__ msgfplus_ + +Requirements +------------ + +This package uses protk_, msgfplus_ and the `idconvert` tool from Proteowizard_ which need to be present in order for the tool to work. + +.. _protk: https://github.com/iracooke/protk +.. _Proteowizard: http://proteowizard.sourceforge.net/ + + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_, msgfplus_ and Proteowizard_ manually are available here_. + +2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed. + +.. _docker: https://www.docker.com/ +.. _here: https://github.com/iracooke/protk/#galaxy-integration +.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker +__ container_ + + +Further Info +------------ + +The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__ + +.. _github: https://github.com/iracooke/protk-galaxytools +.. _issue: https://github.com/iracooke/protk-galaxytools/issues +__ issue_ + + +Information on the MS-GF+ search tool itself can be found here_ + +.. _here: http://proteowizard.sourceforge.net/ + diff -r 32365fec702c -r 6c751c59ce18 msgfplus_search.xml --- a/msgfplus_search.xml Thu Jun 26 11:39:21 2014 -0400 +++ b/msgfplus_search.xml Thu Mar 26 20:04:30 2015 -0400 @@ -1,7 +1,8 @@ - + Run an MSGF+ Search - protk + iracooke/protk-1.4.1 + protk msgfplus proteowizard @@ -45,6 +46,9 @@ --min-pep-charge=$min_pep_charge --num-reported-matches=$num_reported_matches --java-mem=$java_mem + + --threads $threads + #if $pepxml_output_use: --pepxml #end if @@ -94,7 +98,7 @@ Missed Cleavages Allowed - + @@ -116,7 +120,7 @@ Instrument Type - + @@ -137,7 +141,7 @@ - + Precursor Ion Tolerance Units @@ -151,24 +155,33 @@ - + + - + - + + + - - - + + + + + + + + + + **What it does** diff -r 32365fec702c -r 6c751c59ce18 repository_dependencies.xml --- a/repository_dependencies.xml Thu Jun 26 11:39:21 2014 -0400 +++ b/repository_dependencies.xml Thu Mar 26 20:04:30 2015 -0400 @@ -1,4 +1,4 @@ - + diff -r 32365fec702c -r 6c751c59ce18 test-data/testdb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testdb.fasta Thu Mar 26 20:04:30 2015 -0400 @@ -0,0 +1,38 @@ +>sp|ALBU_BOVIN| +MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIA +FSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCK +VASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEF +KADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGAC +LLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAE +FVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE +CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFL +GSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKL +KHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVS +RSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCC 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