remove hardcoded paths in reference setup (b9c351d5) · Commits · github_fork / Universc

README.Rmd

+4 −4

Original line number	Diff line number	Diff line
		@@ -759,11 +759,11 @@ cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2
		cellrangerpath=`which cellranger`

		# set up cellranger reference
		if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		fi
		if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		fi
		cd ..
		```

README.html

+4 −4

Original line number	Diff line number	Diff line
		@@ -343,11 +343,11 @@ cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2
		cellrangerpath=`which cellranger`

		# set up cellranger reference
		if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		fi
		if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		fi
		cd ..</code></pre>
		<p>This creates a reference for Cell Ranger here:</p>

README.md

+4 −4

Original line number	Diff line number	Diff line
		@@ -759,11 +759,11 @@ cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2
		cellrangerpath=`which cellranger`

		# set up cellranger reference
		if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		fi
		if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		fi
		cd ..
		```

test/cellranger_reference/cellranger-tiny-ref/Makefile

+14 −1

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@

		PWD=$(shell pwd)

		all: reference
		all: reference star

		reference:
		@echo "generating cellranger references"
		@@ -19,6 +19,19 @@ reference:
		echo "reference 3.0.0 pre-generated";\
		fi

		star:
		@echo "check for SA files"
		# used to export to PATH for testing on SGE server
		@cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
		@cellrangerpath=`which cellranger`
		# set up cellranger reference
		@if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		fi
		@if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		fi

		##########################################
		# Generic rules
		##########################################

test/run_tests_10x.sh

+4 −4

Original line number	Diff line number	Diff line
		@@ -11,11 +11,11 @@ cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2
		cellrangerpath=`which cellranger`

		# set up cellranger reference
		if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		fi
		if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		fi

		# reset barcodes for test

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