Merge branch 'dev' of github.com:kbattenb/universc into dev (d576f87d) · Commits · github_fork / Universc

launch_universc.sh

+69 −58

Original line number	Original line	Diff line number	Diff line
	@@ -1066,13 +1066,14 @@ if [[ $setup == "false" ]]; then
	fi		fi

	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo " ${#read1[@]} read1s: ${read1[@]}"		echo " Input files prost-curation 1"
	echo " ${#read2[@]} read2s: ${read2[@]}"		echo " ${#read1[@]}files - read1s: ${read1[@]}"
			echo " ${#read2[@]}files - read2s: ${read2[@]}"
	if [[ ${#index1[@]} -gt 0 ]]; then		if [[ ${#index1[@]} -gt 0 ]]; then
	echo " ${#index1[@]} I1s: ${index1[@]}"		echo " ${#index1[@]}files - I1s: ${index1[@]}"
	fi		fi
	if [[ ${#index2[@]} -gt 0 ]]; then		if [[ ${#index2[@]} -gt 0 ]]; then
	echo " ${#index2[@]} I2s: ${index2[@]}"		echo " ${#index2[@]}files - I2s: ${index2[@]}"
	fi		fi
	echo " number of these files are as expected"		echo " number of these files are as expected"
	fi		fi
	@@ -1172,13 +1173,14 @@ for key in ${keys[@]}; do
	done		done

	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo " ${#read1[@]} read1s: ${read1[@]}"		echo " Input files post-curation 2"
	echo " ${#read2[@]} read2s: ${read2[@]}"		echo " ${#read1[@]}files - read1s: ${read1[@]}"
			echo " ${#read2[@]}files - read2s: ${read2[@]}"
	if [[ ${#index1[@]} -gt 0 ]]; then		if [[ ${#index1[@]} -gt 0 ]]; then
	echo " ${#index1[@]} I1s: ${index1[@]}"		echo " ${#index1[@]}files - I1s: ${index1[@]}"
	fi		fi
	if [[ ${#index2[@]} -gt 0 ]]; then		if [[ ${#index2[@]} -gt 0 ]]; then
	echo " ${#index2[@]} I2s: ${index2[@]}"		echo " ${#index2[@]}files - I2s: ${index2[@]}"
	fi		fi
	echo " files exist, with extentions compatible with launch_universc.sh"		echo " files exist, with extentions compatible with launch_universc.sh"
	fi		fi
	@@ -1359,13 +1361,14 @@ for key in ${keys[@]}; do
	done		done

	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo " ${#read1[@]} read1s: ${read1[@]}"		echo " Input files post-curation 3"
	echo " ${#read2[@]} read2s: ${read2[@]}"		echo " ${#read1[@]}files - read1s: ${read1[@]}"
			echo " ${#read2[@]}files - read2s: ${read2[@]}"
	if [[ ${#index1[@]} -gt 0 ]]; then		if [[ ${#index1[@]} -gt 0 ]]; then
	echo " ${#index1[@]} I1s: ${index1[@]}"		echo " ${#index1[@]}files - I1s: ${index1[@]}"
	fi		fi
	if [[ ${#index2[@]} -gt 0 ]]; then		if [[ ${#index2[@]} -gt 0 ]]; then
	echo " ${#index2[@]} I2s: ${index2[@]}"		echo " ${#index2[@]}files - I2s: ${index2[@]}"
	fi		fi
	echo " names of these files are compatible with launch_universc.sh"		echo " names of these files are compatible with launch_universc.sh"
	fi		fi
	@@ -1536,13 +1539,14 @@ if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]] \|\| [
	fi		fi

	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo " ${#read1[@]} read1s: ${read1[@]}"		echo " Input files post-curation 4"
	echo " ${#read2[@]} read2s: ${read2[@]}"		echo " ${#read1[@]}files - read1s: ${read1[@]}"
			echo " ${#read2[@]}files - read2s: ${read2[@]}"
	if [[ ${#index1[@]} -gt 0 ]]; then		if [[ ${#index1[@]} -gt 0 ]]; then
	echo " ${#index1[@]} I1s: ${index1[@]}"		echo " ${#index1[@]}files - I1s: ${index1[@]}"
	fi		fi
	if [[ ${#index2[@]} -gt 0 ]]; then		if [[ ${#index2[@]} -gt 0 ]]; then
	echo " ${#index2[@]} I2s: ${index2[@]}"		echo " ${#index2[@]}files - I2s: ${index2[@]}"
	fi		fi
	echo " input files adjusted for technology-specific conditions"		echo " input files adjusted for technology-specific conditions"
	fi		fi
	@@ -1560,12 +1564,12 @@ elif [[ ${#index1[@]} -gt 0 ]]; then
	fi		fi

	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo "reads:" ${read12[@]}		echo "files to be curated:" ${read12[@]}
	fi		fi

	for fq in "${read12[@]}"; do		for fq in "${read12[@]}"; do
	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo "read: $fq"		echo " read file: $fq"
	fi		fi
	name=`basename $fq`		name=`basename $fq`
	name=${name%.*}		name=${name%.*}
	@@ -1590,13 +1594,16 @@ for fq in "${read12[@]}"; do
	exit 1		exit 1
	fi		fi

	if [[ $verbose == true ]]; then		if [[ $verbose ]]; then
	echo "SAMPLE: $SAMPLE"		echo " $sn(extracted from file) <- $fq"
	echo "sample (field): $sn"		echo " SAMPLE NAME: $SAMPLE"
	fi		fi

	if [[ ${sn} != $SAMPLE ]]; then		if [[ ${sn} != $SAMPLE ]]; then
	if [[ -z $SAMPLE ]]; then		if [[ -z $SAMPLE ]]; then
			if [[ $verbose ]]; then
			echo " setting SAMPLE NAME to ${sn}"
			fi
	SAMPLE=${sn}		SAMPLE=${sn}
	else		else
	echo "Error: some samples are labeled $SAMPLE while others are labeled $sn. cellranger can only handle files from one sample at a time."		echo "Error: some samples are labeled $SAMPLE while others are labeled $sn. cellranger can only handle files from one sample at a time."
	@@ -1832,7 +1839,7 @@ fi



	#####check if reference is present#####		####check if reference is present#####
	if [[ -z $reference ]]; then		if [[ -z $reference ]]; then
	if [[ $setup == "false" ]] \|\| [[ ${#read1[@]} -ne 0 ]] \|\| [[ ${#read2[@]} -ne 0 ]]; then		if [[ $setup == "false" ]] \|\| [[ ${#read1[@]} -ne 0 ]] \|\| [[ ${#read2[@]} -ne 0 ]]; then
	echo "Error: option --reference is required";		echo "Error: option --reference is required";
	@@ -1935,6 +1942,7 @@ crIN=${crIN}_${id}
	##########		##########



	#####checking if crIN exists#####		#####checking if crIN exists#####
	if [[ ! -d $crIN ]]; then		if [[ ! -d $crIN ]]; then
	convert=true		convert=true
	@@ -2107,6 +2115,7 @@ if [[ $lock -eq 0 ]]; then
	sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py		sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py
	fi		fi
	fi		fi

	#backup 10x navbar		#backup 10x navbar
	if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ]];then		if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ]];then
	cp ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html		cp ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html
	@@ -2120,6 +2129,7 @@ if [[ $lock -eq 0 ]]; then
	if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ]];then		if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ]];then
	cp ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html		cp ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html
	fi		fi

	#restore cloupe generation		#restore cloupe generation
	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo "restore cloupe"		echo "restore cloupe"
	@@ -2134,6 +2144,7 @@ if [[ $lock -eq 0 ]]; then
	echo "sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro"		echo "sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro"
	fi		fi
	sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro		sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

	#restore 11 lines for cloupe preprocess call (all following steps are needed to be called together or the call will break)		#restore 11 lines for cloupe preprocess call (all following steps are needed to be called together or the call will break)
	##restore defining CLOUPE_PREPROCESS		##restore defining CLOUPE_PREPROCESS
	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	@@ -2144,8 +2155,7 @@ if [[ $lock -eq 0 ]]; then
	sed -i '/output_for_cloupe/s/^##//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro		sed -i '/output_for_cloupe/s/^##//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
	##remove calling CLOUPE_PREPROCESS		##remove calling CLOUPE_PREPROCESS
	### iterate over all files calling CLOUPE_PREPROCESS		### iterate over all files calling CLOUPE_PREPROCESS
	for file in $(grep -l "call CLOUPE_PREPROCESS" ${cellrangerpath}-cs/${cellrangerversion}/mro/*.mro )		for file in $(grep -l "call CLOUPE_PREPROCESS" ${cellrangerpath}-cs/${cellrangerversion}/mro/*.mro ); do
	do
	#find start of CLOUPE_PREPROCESS call		#find start of CLOUPE_PREPROCESS call
	num=$(grep -n "call CLOUPE_PREPROCESS" $file \| head -n 1 \| cut -d":" -f1)		num=$(grep -n "call CLOUPE_PREPROCESS" $file \| head -n 1 \| cut -d":" -f1)
	#find end of CLOUPE_PREPROCESS call		#find end of CLOUPE_PREPROCESS call
	@@ -2161,6 +2171,7 @@ if [[ $lock -eq 0 ]]; then
	#line of HTML in header is removed		#line of HTML in header is removed
	sed '/class="logo"/d' ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html > ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html		sed '/class="logo"/d' ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html > ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html
	fi		fi

	#disable cloupe generation		#disable cloupe generation
	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo "disable cloupe"		echo "disable cloupe"

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