Merge pull request #323 from NelleV/fix_ex

FIX ice is now picked up globally and not locally
nservant · Mar 25, 2020 · 88c0452 · 88c0452
2 parents 9a0bdcd + 2e97fae
commit 88c0452
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/Makefile b/Makefile
@@ -54,10 +54,10 @@ readstrimming: $(INST_SOURCES)/cutsite_trimming.cpp
 iced: $(INST_SOURCES)/ice_mod
 ifeq ("$(RUNNER)","root")
 	@echo "Installing the iced package as root"     
-	(cp $(INST_SOURCES)/ice_mod/iced/scripts/ice ${INST_SCRIPTS}; cd $(INST_SOURCES)/ice_mod/; ${PYTHON_PATH}/python setup.py install;)
+	(cd $(INST_SOURCES)/ice_mod/; ${PYTHON_PATH}/python setup.py install;)
 else
 	@echo "Installing the iced package in --user repository [runner=$(RUNNER)]"
-	(cp $(INST_SOURCES)/ice_mod/iced/scripts/ice ${INST_SCRIPTS}; cd $(INST_SOURCES)/ice_mod/; ${PYTHON_PATH}/python setup.py install --user;)
+	(cd $(INST_SOURCES)/ice_mod/; ${PYTHON_PATH}/python setup.py install --user;)
 endif
 
 test: config_check

diff --git a/scripts/ice_norm.sh b/scripts/ice_norm.sh
@@ -78,7 +78,7 @@ do
 	    then
 		input=$(find -L $IN_DIR/${RES_FILE_NAME}/ -name "*_$bsize.matrix*" ! -name "*iced*")
 		if [ ! -z $input ]; then
-		    cmd="${PYTHON_PATH}/python ${SCRIPTS}/ice --results_filename ${NORM_DIR}/${bsize}/${RES_FILE_NAME}_${bsize}_iced.matrix --filter_low_counts_perc ${FILTER_LOW_COUNT_PERC} --filter_high_counts_perc ${FILTER_HIGH_COUNT_PERC} --max_iter ${MAX_ITER} --eps ${EPS} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${input}"
+		    cmd="ice --results_filename ${NORM_DIR}/${bsize}/${RES_FILE_NAME}_${bsize}_iced.matrix --filter_low_counts_perc ${FILTER_LOW_COUNT_PERC} --filter_high_counts_perc ${FILTER_HIGH_COUNT_PERC} --max_iter ${MAX_ITER} --eps ${EPS} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${input}"
                     exec_cmd $cmd >> ${ldir}/ice_${bsize}.log
                 else
 		    echo "Warning : Matrix not found at $bsize resolution in $IN_DIR/${RES_FILE_NAME} - skip"
@@ -87,7 +87,7 @@ do
 		for r in $(find -L ${IN_DIR}/${RES_FILE_NAME}/raw/${bsize}/ -name "*_$bsize.matrix*")
 		do
 		    ofile=$(basename ${r} | sed -e 's/.matrix/_iced.matrix/')
-		    cmd="${PYTHON_PATH}/python ${SCRIPTS}/ice --results_filename ${NORM_DIR}/${bsize}/${ofile} --filter_low_counts_perc ${FILTER_LOW_COUNT_PERC} --filter_high_counts_perc ${FILTER_HIGH_COUNT_PERC} --max_iter ${MAX_ITER} --eps ${EPS} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${r}"
+		    cmd="ice --results_filename ${NORM_DIR}/${bsize}/${ofile} --filter_low_counts_perc ${FILTER_LOW_COUNT_PERC} --filter_high_counts_perc ${FILTER_HIGH_COUNT_PERC} --max_iter ${MAX_ITER} --eps ${EPS} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${r}"
 		    exec_cmd $cmd >> ${ldir}/ice_${bsize}.log 2>&1
 		done
 	    fi

diff --git a/scripts/make_slurm_script.sh b/scripts/make_slurm_script.sh
@@ -120,7 +120,7 @@ then
 
 #SBATCH --mail-user=${JOB_MAIL}
 #SBATCH --mail-type=end
-#SBATCH --job-name=HiCpro_s1_${JOB_NAME}
+#SBATCH --job-name=HiCpro_s2_${JOB_NAME}
 #SBATCH --export=ALL
 
 cd \$SLURM_SUBMIT_DIR