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annotate umiout.sh @ 2:178ebdfe5a7e draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
author bgruening
date Tue, 15 Oct 2019 12:01:50 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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diff changeset
1 #!/usr/bin/bash
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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diff changeset
2
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
3 mkdir fixed;
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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diff changeset
4 for file in ./umiout/*;
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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diff changeset
5 do prefix="${file%.dot.gz}";
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
6 prefix=${prefix/.\/umiout\//};
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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7 gunzip $file;
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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8 sed "s/umiout\/$prefix.dot.gz/$prefix/" umiout/$prefix.dot > fixed/$prefix.dot;
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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diff changeset
9 dot -Tpdf fixed/$prefix.dot -o fixed/$prefix.pdf;
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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10 done
178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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diff changeset
11 ls fixed