Mercurial > repos > bgruening > repeat_masker

comparison repeatmasker.xml @ 9:438f65cb1d14 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"
author iuc
date Tue, 18 Aug 2020 05:39:55 -0400
parents ade773848c3d
children bfc70c8cc5ca
comparison
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8:ade773848c3d 9:438f65cb1d14
1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01"> 1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.9" profile="17.01">
2 <description>screen DNA sequences for interspersed repeats and low complexity regions</description> 2 <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="4.0.7">repeatmasker</requirement> 5 <requirement type="package" version="4.0.9_p2">repeatmasker</requirement>
6 </requirements> 6 </requirements>
7 7
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 RM_PATH=\$(which RepeatMasker) && 9 RM_PATH=\$(which RepeatMasker) &&
10 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi && 10 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
11 RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries && 11 RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
12 mkdir lib && 12 mkdir lib &&
13 export REPEATMASKER_LIB_DIR=\$(pwd)/lib && 13 export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
14 for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done && 14 for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&