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Workaround for gzip support breaking on Galaxy 16.01
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See galaxyproject/tools-iuc#1373
which was fixed and back-ported to Galaxy 16.07,
galaxyproject/galaxy#4224
galaxyproject/galaxy#4230

This would still break with other non-compressed FASTA
subclasses, but this is intended as a stop-gap until
the last few elderly Galaxy servers in use are updated.
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peterjc committed Oct 22, 2018
1 parent 229de98 commit 971050f
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions tools/ncbi_blast_plus/ncbi_macros.xml
Original file line number Diff line number Diff line change
Expand Up @@ -567,7 +567,7 @@
<token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token>

<token name="@QUERY@"><![CDATA[
#if $query.is_of_type('fasta.gz'):
#if $query.is_of_type('fasta.gz') and $query.ext != "fasta":
-query <(gunzip -c '${query}')
#else:
-query '${query}'
Expand All @@ -580,7 +580,7 @@
#elif $db_opts.db_opts_selector == "histdb":
-db '${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}'
#else:
#if $db_opts.subject.is_of_type('fasta.gz'):
#if $db_opts.subject.is_of_type('fasta.gz') and $db_opts.subject.ext != "fasta":
-subject <(gunzip -c '${$db_opts.subject}')
#else:
-subject '${db_opts.subject}'
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