correct Makefile and paths for test references (ec32f5e2) · Commits · github_fork / Universc

README.Rmd

+4 −6

Original line number	Diff line number	Diff line
		@@ -754,18 +754,16 @@ imported from an existing reference. The following code detects whether the refe
		available in an existing cellranger installation.

		```
		cd test
		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
		if [[ ! -f test/cellranger_reference/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 test/cellranger_reference/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
		if [[ ! -f test/cellranger_reference/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 test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
		fi
		cd ..
		```

		This creates a reference for Cell Ranger here:

test/cellranger_reference/cellranger-tiny-ref/Makefile

+7 −11

Original line number	Diff line number	Diff line
		@@ -19,18 +19,14 @@ reference:
		echo "reference 3.0.0 pre-generated";\
		fi

		cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
		cellrangerpath=`which cellranger`
		cellrangerdir=$$(dirname $$(which cellranger))

		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
		@echo $(cellrangerdir) $(cellrangerpath) $(cellrangerversion)
		bash import_SA.sh

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

test/cellranger_reference/cellranger-tiny-ref/import_SA.sh

0 → 100644

+16 −0

Original line number	Diff line number	Diff line
		#! /bin/bash

		cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
		cellrangerpath=`which cellranger`
		cellrangerdir=$(dirname $(which cellranger))

		#echo "check for SA files"
		echo $cellrangerdir $cellrangerpath $cellrangerversion
		if [[ ! -f 3.0.0/star/SA ]] && [[ -f ${cellrangerpathdir}/cellranger-tiny-ref/3.0.0/star/SA ]]; then
		rsync ${cellrangerdir}/cellranger-tiny-ref/3.0.0/star/SA 3.0.0/star/SA
		fi
		if [[ ! -f 1.2.0/star/SA ]] && [[ -f ${cellrangerdir}/cellranger-tiny-ref/1.2.0/star/SA ]]; then
		rsync ${cellrangerdir}/cellranger-tiny-ref/1.2.0/star/SA 1.2.0/star/SA
		fi
		touch 3.0.0/star/SA
		touch 1.2.0/star/SA

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 ${cellrangerpath}-${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
		if [[ ! -f cellranger_reference/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 cellranger_reference/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
		if [[ ! -f cellranger_reference/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 cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
		fi

		# reset barcodes for test

test/run_tests_dropseq.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 ${cellrangerpath}-${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
		if [[ ! -f cellranger_reference/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 cellranger_reference/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
		if [[ ! -f cellranger_reference/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 cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
		fi

		## test drop-seq data

Admin message