Mercurial > repos > jjohnson > defuse8

annotate config_sub.sh @ 1:e0a835a2f74a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 1a82c0609363fe0541e6dbdd46308a67f30ca9e1-dirty
author jjohnson
date Mon, 20 May 2019 15:30:06 -0400
parents 63f23d5db27c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
1 #!/bin/bash
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
2 ## substitute pathnames into config file
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
3 #!/bin/bash
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
4 SAMTOOLS_BIN=`which samtools`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
5 BOWTIE_BIN=`which bowtie`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
6 BOWTIE_BUILD_BIN=`which bowtie-build`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
7 BLAT_BIN=`which blat`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
8 FATOTWOBIT_BIN=`which faToTwoBit`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
9 GMAP_BIN=`which gmap`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
10 GMAP_BUILD_BIN=`which gmap_build`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
11 GMAP_SETUP_BIN=$GMAP_BUILD_BIN
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
12 R_BIN=`which R`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
13 RSCRIPT_BIN=`which Rscript`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
14 DEFUSE_BIN=`which defuse_run.pl`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
15 DEFUSE_PATH=`python -c "import os.path; print(os.path.dirname(os.path.dirname(os.path.realpath(\"$DEFUSE_BIN\"))))"`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
16 cat $1 | sed "s#__DEFUSE_PATH__#${DEFUSE_PATH}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
17 sed "s#__SAMTOOLS_BIN__#${SAMTOOLS_BIN}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
18 sed "s#__BOWTIE_BIN__#${BOWTIE_BIN}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
19 sed "s#__BOWTIE_BUILD_BIN__#${BOWTIE_BUILD_BIN}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
20 sed "s#__BLAT_BIN__#${BLAT_BIN}#"| \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
21 sed "s#__FATOTWOBIT_BIN__#${FATOTWOBIT_BIN}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
22 sed "s#__GMAP_BIN__#${GMAP_BIN}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
23 sed "s#^gmap_setup_bin#gmap_build_bin#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
24 sed "s#__GMAP_SETUP_BIN__#${GMAP_SETUP_BIN}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
25 sed "s#__GMAP_BUILD_BIN__#${GMAP_BUILD_BIN}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
26 sed "s#__R_BIN__#${R_BIN}#" | \
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
27 sed "s#__RSCRIPT_BIN__#${RSCRIPT_BIN}#" > $2
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
28 export DATASET_DIRECTORY=`grep '^dataset_directory' $1 | awk '{print \$NF}'`
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
29 echo "$DATASET_DIRECTORY"