Mercurial > repos > bgruening > repeat_masker

comparison repeatmasker.xml @ 10:d6433d4614fb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 2f2463888c41a99aec46d4da0eb0ac66cbc20889"
author iuc
date Fri, 27 Aug 2021 09:15:28 +0000
parents c348c911a415
children fa311361317b
comparison
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9:c348c911a415 10:d6433d4614fb
9 <version_command>repeatmasker --version</version_command> 9 <version_command>repeatmasker --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 RM_PATH=\$(which RepeatMasker) && 11 RM_PATH=\$(which RepeatMasker) &&
12 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi && 12 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
13 13
14 RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries && 14 if [ -z "\$RM_LIB_PATH" ] ; then RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries ; fi &&
15 #if $repeat_source.source_type == "dfam_up": 15 #if $repeat_source.source_type == "dfam_up":
16 mkdir lib/ && 16 mkdir lib/ &&
17 ln -s '${repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 && 17 ln -s '${repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 &&
18 RM_LIB_PATH=\$(pwd)/lib && 18 RM_LIB_PATH=\$(pwd)/lib &&
19 #end if 19 #end if