Mercurial > repos > jjohnson > defuse
diff defuse.xml @ 8:57841f58676f draft
Add gmap_bin to defuse.xml configfile generation
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Sun, 13 Jan 2013 13:48:56 -0600 |
| parents | 1ea6445491d4 |
| children | 9f30de0ff090 |
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--- a/defuse.xml Mon Jan 07 14:52:26 2013 -0600 +++ b/defuse.xml Sun Jan 13 13:48:56 2013 -0600 @@ -191,6 +191,12 @@ #except __FATOTWOBIT_BIN__ #end try +gmap_bin = #slurp +#try +$ref_dict['gmap_bin'] +#except +__GMAP_BIN__ +#end try r_bin = #slurp #try $ref_dict['r_bin'] @@ -552,6 +558,7 @@ if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi +if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi