| Previous changeset 2:3c5f10f7dd40 (2015-11-27) Next changeset 4:89315bdc1a8c (2018-09-26) |
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Commit message:
Uploaded v2.0.2 (use conda for dependency resolution) |
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modified:
README.rst weeder2_wrapper.xml |
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added:
weeder2_macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r 3c5f10f7dd40 -r f19e18ab01b1 README.rst --- a/README.rst Fri Nov 27 11:06:28 2015 -0500 +++ b/README.rst Mon Mar 05 10:19:50 2018 -0500 |
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| @@ -79,6 +79,7 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +2.0.2 - Drop ``tool_dependencies.xml`` & use conda to resolve dependencies 2.0.1 - Explicitly specify frequency files in ``weeder2.loc``. 2.0.0 - Initial version ========== ====================================================================== |
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| diff -r 3c5f10f7dd40 -r f19e18ab01b1 tool_dependencies.xml --- a/tool_dependencies.xml Fri Nov 27 11:06:28 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,39 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="weeder" version="2.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://159.149.160.51/modtools/downloads/weeder2.0.tar.gz</action> - <action type="shell_command"> - g++ weeder2.cpp -o weeder2 -O3 - </action> - <!-- Move weeder2 executable --> - <action type="move_file"> - <source>weeder2</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <!-- Move data files --> - <action type="move_directory_files"> - <source_directory>FreqFiles</source_directory> - <destination_directory>$INSTALL_DIR/FreqFiles</destination_directory> - </action> - <!-- Set environment variables --> - <action type="set_environment"> - <environment_variable name="WEEDER_DIR" action="set_to">$INSTALL_DIR</environment_variable> - </action> - <action type="set_environment"> - <environment_variable name="WEEDER_FREQFILES_DIR" action="set_to">$INSTALL_DIR/FreqFiles</environment_variable> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>Installs Weeder 2.0 - - See http://159.149.160.51/modtools/downloads/weeder2.html - and http://159.149.160.51/modtools/ - </readme> - </package> -</tool_dependency> - |
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| diff -r 3c5f10f7dd40 -r f19e18ab01b1 weeder2_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/weeder2_macros.xml Mon Mar 05 10:19:50 2018 -0500 |
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| @@ -0,0 +1,6 @@ +<macros> + <!-- + Set the path for the weeder2 data files + --> + <token name="@CONDA_WEEDER2_FREQFILES_PATH@">if [ -z "\$WEEDER_FREQFILES_DIR" ]; then export WEEDER_FREQFILES_DIR=\$(dirname \$(readlink -e \$(which weeder2)))/FreqFiles; fi</token> +</macros> |
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| diff -r 3c5f10f7dd40 -r f19e18ab01b1 weeder2_wrapper.xml --- a/weeder2_wrapper.xml Fri Nov 27 11:06:28 2015 -0500 +++ b/weeder2_wrapper.xml Mon Mar 05 10:19:50 2018 -0500 |
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| @@ -1,9 +1,14 @@ -<tool id="motiffinding_weeder2" name="Weeder2" version="2.0.1"> +<tool id="motiffinding_weeder2" name="Weeder2" version="2.0.2"> <description>Motif discovery in sequences from coregulated genes of a single species</description> + <macros> + <import>weeder2_macros.xml</import> + </macros> <requirements> <requirement type="package" version="2.0">weeder</requirement> </requirements> - <command interpreter="bash">weeder2_wrapper.sh + <command><![CDATA[ + @CONDA_WEEDER2_FREQFILES_PATH@ && + bash $__tool_directory__/weeder2_wrapper.sh $sequence_file $species_code ${species_code.fields.path} $output_motifs_file $output_matrix_file $strands @@ -16,7 +21,7 @@ -sim $advanced_options.sim_threshold -em $advanced_options.em_cycles #end if - </command> + ]]></command> <inputs> <param name="sequence_file" type="data" format="fasta" label="Input sequence" /> <param name="species_code" type="select" label="Species to use for background comparison"> |