Mercurial > repos > mvdbeek > bam_tag_reads

annotate test.sh @ 1:8138277ea0e5 draft

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planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
author mvdbeek
date Wed, 08 Feb 2017 03:36:05 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
1 #!/usr/bin/env bash
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
2
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
3 set -e
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
4
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
5 if grep -v 'python tag_reads.py' bam_tag_reads.xml
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
6 then
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
7 sed -i.bak 's/tag_reads -t/python \$__tool_directory__\/tag_reads.py -t/g' bam_tag_reads.xml
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
8 fi
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
9 cp ../tag_reads/tag_reads.py .
8138277ea0e5 planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit e4243f5ba5d89a06c1ae68cc49d830f1b6e9cb46
mvdbeek
parents:
diff changeset
10 planemo test --conda_prefix ~/miniconda3