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annotate umiout.sh @ 19:15cd64d7c58b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26cff0d523671ac1e56ba7ef4965861b387727e8
author bgruening
date Fri, 23 Jun 2023 17:02:35 +0000
parents 7fdb9d1591e2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
1 #!/usr/bin/bash
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
2
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
3 mkdir fixed;
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
4 for file in ./umiout/*;
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
5 do prefix="${file%.dot.gz}";
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
6 prefix=${prefix/.\/umiout\//};
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
7 gunzip $file;
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
8 sed "s/umiout\/$prefix.dot.gz/$prefix/" umiout/$prefix.dot > fixed/$prefix.dot;
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
9 dot -Tpdf fixed/$prefix.dot -o fixed/$prefix.pdf;
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
10 done
7fdb9d1591e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
11 ls fixed