| Previous changeset 14:038a5210392a (2017-12-12) Next changeset 16:bdd93719cede (2017-12-18) |
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Commit message:
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modified:
create_reference_dataset.xml datamanager_create_reference.xml |
| b |
| diff -r 038a5210392a -r b67c24d902aa create_reference_dataset.xml --- a/create_reference_dataset.xml Tue Dec 12 10:02:00 2017 -0500 +++ b/create_reference_dataset.xml Tue Dec 12 12:00:24 2017 -0500 |
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| @@ -190,6 +190,7 @@ fatotwobit_bin = __FATOTWOBIT_BIN__ gmap_bin = __GMAP_BIN__ gmap_setup_bin = __GMAP_SETUP_BIN__ +gmap_build_bin = __GMAP_BUILD_BIN__ r_bin = __R_BIN__ rscript_bin = __RSCRIPT_BIN__ @@ -259,6 +260,7 @@ 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 __GMAP_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BUILD_BIN=`which gmap_build`;then sed -i'.tmp' "s#__GMAP_BUILD_BIN__#\${GMAP_BUILD_BIN}#" $defuse_config; fi if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $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 |
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| diff -r 038a5210392a -r b67c24d902aa datamanager_create_reference.xml --- a/datamanager_create_reference.xml Tue Dec 12 10:02:00 2017 -0500 +++ b/datamanager_create_reference.xml Tue Dec 12 12:00:24 2017 -0500 |
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| @@ -191,6 +191,7 @@ fatotwobit_bin = __FATOTWOBIT_BIN__ gmap_bin = __GMAP_BIN__ gmap_setup_bin = __GMAP_SETUP_BIN__ +gmap_build_bin = __GMAP_BUILD_BIN__ r_bin = __R_BIN__ rscript_bin = __RSCRIPT_BIN__ @@ -261,9 +262,8 @@ 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 __GMAP_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BUILD_BIN=`which gmap_build`;then sed -i'.tmp' "s#__GMAP_BUILD_BIN__#\${GMAP_BUILD_BIN}#" $defuse_config; fi if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $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 ## copy config to output cp $defuse_config \$1/defuse_config.txt ## Run the create_reference_dataset.pl |