Mercurial > repos > bgruening > antismash
changeset 24:b942dfd80819 draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 15 Oct 2013 04:19:33 -0400 |
| parents | d26e8aa37ce9 |
| children | 99435bb90725 |
| files | antismash.xml src/genecluster_sequence/__init__.py tool_dependencies.xml |
| diffstat | 3 files changed, 56 insertions(+), 65 deletions(-) [+] |
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--- a/antismash.xml Mon Oct 14 04:36:52 2013 -0400 +++ b/antismash.xml Tue Oct 15 04:19:33 2013 -0400 @@ -41,7 +41,6 @@ --disable-embl --outputfolder $outputfolder - #echo 'input_tempfile.' + $file_extension# ## leave out the start and end features, it can be easily replaced with Galaxy tools @@ -53,16 +52,16 @@ ## html output #if 'html' in str($outputs).split(','): - cp #echo os.path.join($outputfolder, 'index.html')# $html; + cp #echo os.path.join($outputfolder, 'index.html')# $html 2>/dev/null; #end if ## gene clusters #if 'geneclusterprots_tabular' in str($outputs).split(','): - cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular; + cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular 2>/dev/null; #end if #if 'geneclusterprots_fasta' in str($outputs).split(','): - cp #echo os.path.join($outputfolder, '*_genecluster_proteins.fa')# $geneclusterprots_fasta; + cp #echo os.path.join($outputfolder, '*_genecluster_proteins.fa')# $geneclusterprots_fasta 2>/dev/null; #end if @@ -70,7 +69,7 @@ #if 'archive_svgs' in str($outputs).split(','): cd #echo os.path.join($outputfolder, 'svg')#; #if $clusterblast: - tar cfz $archive_svgs *_all.svg genecluster*; + tar cfz $archive_svgs *_all.svg genecluster* 2>/dev/null; #else: tar cfz $archive_svgs genecluster*; #end if @@ -79,12 +78,12 @@ ##all files in a archive #if 'archive' in str($outputs).split(','): cd $outputfolder; - tar cf $archive *.zip; + tar cf $archive *.zip 2>/dev/null; #end if ## genbank #if 'gb' in str($outputs).split(','): - cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank; + cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2>/dev/null; #end if </command>
--- a/src/genecluster_sequence/__init__.py Mon Oct 14 04:36:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -#!/usr/bin/env python - -""" - antiSMASH 2.0 output plugin to write all cluster proteins to a file (*_genecluster_proteins.fa) -""" -import logging -from os import path -from antismash import utils - -name = "genecluster_proteins" -short_description = "Ouptut gene clusters as FASTA sequences" -# Output plugins are sorted by priority, lower numbers get run first -priority = 9 - -def write(seq_records, options): - """Write all cluster proteins to a file - - Args: - seq_records (iterable): An iterable containing Bio.SeqRecords - options (argparse.Namespace): The options passed to the program - """ - basename = seq_records[0].id - output_name = path.join(options.outputfoldername, "%s_genecluster_proteins.fa" % basename) - logging.debug("Writing seq_records to %r" % output_name) - - with open(output_name, 'w+') as handle: - for seq_record in seq_records: - clusters = utils.get_cluster_features(seq_record) - for cluster in clusters: - clustertype = utils.get_cluster_type(cluster) - clusternr = utils.get_cluster_number(cluster) - for feature in utils.get_cluster_cds_features(cluster, seq_record): - qual = feature.qualifiers - fasta_header = '>%s:%s %s #%s - %s\n' % (qual['locus_tag'][0], qual['protein_id'][0], clustertype, clusternr, qual['product'][0]) - handle.write( fasta_header ) - handle.write( '%s\n' % qual['translation'][0] ) - -
--- a/tool_dependencies.xml Mon Oct 14 04:36:52 2013 -0400 +++ b/tool_dependencies.xml Tue Oct 15 04:19:33 2013 -0400 @@ -13,7 +13,6 @@ <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="helperlibs" version="0.1.2"> <install version="1.0"> <actions> @@ -84,7 +83,8 @@ <package name="antismash" version="2.0.2"> <install version="1.0"> <actions_group> - <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. --> + + <!-- Download the binaries for antiSMASH compatible with 64-bit OSX. --> <actions architecture="x86_64" os="darwin"> <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action> <action type="move_directory_files"> @@ -94,6 +94,43 @@ <action type="chmod"> <file mode="750">$INSTALL_DIR/run_antismash.py</file> </action> + <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and + we need to copy this plugin into the correct location. + --> + <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action> + <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action> + <action type="move_file"> + <source>__init__.py</source> + <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination> + </action> + <!-- AntiSmash has a prerequirement check that is not useful for us, because we + do not offer the option for genprediction and do not install glimmer and Co. + For that reason deactivate the check. + --> + <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action> + <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> + <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>n> + </actions> + + <!-- Download the binaries for antiSMASH compatible with 64-bit OSX. --> + <actions architecture="i386" os="darwin"> + <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="chmod"> + <file mode="750">$INSTALL_DIR/run_antismash.py</file> + </action> + <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and + we need to copy this plugin into the correct location. + --> + <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action> + <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action> + <action type="move_file"> + <source>__init__.py</source> + <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination> + </action> <!-- AntiSmash has a prerequirement check that is not useful for us, because we do not offer the option for genprediction and do not install glimmer and Co. For that reason deactivate the check. @@ -102,24 +139,7 @@ <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> </actions> - <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. --> - <actions architecture="i386" os="darwin"> - <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - <action type="chmod"> - <file mode="750">$INSTALL_DIR/run_antismash.py</file> - </action> - <!-- AntiSmash has a prerequirement check that is not useful for us, because we - do not offer the option for genprediction and do not install glimmer and Co. - For that reason deactivate the check. - --> - <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action> - <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> - <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> - </actions> + <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. --> <actions architecture="x86_64" os="linux"> <action target_filename="antismash-2.0.2.tar.bz2" type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2</action> @@ -147,6 +167,7 @@ <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> </actions> + <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. --> <actions architecture="i386" os="linux"> <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2</action> @@ -157,6 +178,15 @@ <action type="chmod"> <file mode="750">$INSTALL_DIR/run_antismash.py</file> </action> + <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and + we need to copy this plugin into the correct location. + --> + <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action> + <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action> + <action type="move_file"> + <source>__init__.py</source> + <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination> + </action> <!-- AntiSmash has a prerequirement check that is not useful for us, because we do not offer the option for genprediction and do not install glimmer and Co. For that reason deactivate the check.