Mercurial > repos > bgruening > repeat_masker
comparison repeatmasker.xml @ 9:438f65cb1d14 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"
author | iuc |
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date | Tue, 18 Aug 2020 05:39:55 -0400 |
parents | ade773848c3d |
children | bfc70c8cc5ca |
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8:ade773848c3d | 9:438f65cb1d14 |
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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 && |