Mercurial > repos > bgruening > antismash
changeset 23:d26e8aa37ce9 draft
Uploaded
author | bgruening |
---|---|
date | Mon, 14 Oct 2013 04:36:52 -0400 |
parents | 225d40beff1a |
children | b942dfd80819 |
files | antismash.xml repository_dependencies.xml tool_dependencies.xml |
diffstat | 3 files changed, 17 insertions(+), 8 deletions(-) [+] |
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--- a/antismash.xml Mon Oct 14 03:26:11 2013 -0400 +++ b/antismash.xml Mon Oct 14 04:36:52 2013 -0400 @@ -14,7 +14,10 @@ <command> #import os, glob #set $outputfolder = $html.files_path - #if $infile.ext == 'genbank': + #if str($infile.ext) == 'genbank': + #set $file_extension = 'gb' + #else: + ## TODO add embl as input file #set $file_extension = 'gb' #end if
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Oct 14 04:36:52 2013 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="AntiSmash requires the Galaxy applicable data formats used by Emboss tools, especially genbank."> + <repository changeset_revision="9f36ad2af086" name="emboss_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +</repositories>
--- a/tool_dependencies.xml Mon Oct 14 03:26:11 2013 -0400 +++ b/tool_dependencies.xml Mon Oct 14 04:36:52 2013 -0400 @@ -130,6 +130,15 @@ <action type="chmod"> <file mode="750">$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. @@ -137,13 +146,6 @@ <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 $INSTALL_DIR/antismash/generic_modules/clusterblast</action> - <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and - we need to copy this plugin into the correct location. - --> - <action type="move_directory_files"> - <source_directory>$REPOSITORY_INSTALL_DIR/src/</source_directory> - <destination_directory>$INSTALL_DIR/antismash/output_modules/</destination_directory> - </action> </actions> <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. --> <actions architecture="i386" os="linux">