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annotate umiout.sh @ 4:362ba03406b4 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
author bgruening
date Mon, 13 Jul 2020 21:12:37 +0000
parents 7c618ec039b8
children 58b9ef13fcca
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
1 #!/usr/bin/bash
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
2
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
3 mkdir fixed;
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
4 for file in ./umiout/*;
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
5 do prefix="${file%.dot.gz}";
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
6 prefix=${prefix/.\/umiout\//};
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
7 gunzip $file;
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
8 sed "s/umiout\/$prefix.dot.gz/$prefix/" umiout/$prefix.dot > fixed/$prefix.dot;
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
9 dot -Tpdf fixed/$prefix.dot -o fixed/$prefix.pdf;
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
10 done
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
11 ls fixed