Mercurial > repos > jjohnson > defuse
changeset 9:9f30de0ff090 draft
Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 14 Jan 2013 11:26:17 -0600 |
| parents | 57841f58676f |
| children | f65857c1b92e |
| files | defuse.xml |
| diffstat | 1 files changed, 22 insertions(+), 0 deletions(-) [+] |
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--- a/defuse.xml Sun Jan 13 13:48:56 2013 -0600 +++ b/defuse.xml Mon Jan 14 11:26:17 2013 -0600 @@ -197,6 +197,18 @@ #except __GMAP_BIN__ #end try +gmap_bin = #slurp +#try +$ref_dict['gmap_bin'] +#except +__GMAP_BIN__ +#end try +gmap_setup_bin = #slurp +#try +$ref_dict['gmap_setup_bin'] +#except +__GMAP_SETUP_BIN__ +#end try r_bin = #slurp #try $ref_dict['r_bin'] @@ -210,6 +222,15 @@ __RSCRIPT_BIN__ #end try +# Directory where you want your dataset +gmap_index_directory = #slurp +#try +$ref_dict['gmap_index_directory'] +#except +$(dataset_directory)/gmap +#end try + + #raw # Dataset files dataset_prefix = $(dataset_directory)/defuse @@ -559,6 +580,7 @@ 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 __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_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