Loading README.md +69 −0 Original line number Diff line number Diff line Loading @@ -120,6 +120,16 @@ This script will run in bash on any OS (but it has only been tested on Linux Deb with this configuration requires a lot of memory (40Gb) so running on server is recommended. SGE job modes are supported to run cellranger with multiple threads. -> migrate to Makefile? ### System Requirements ...Unix systems with cellranger installed. ### Docker image ... ## Usage <span id="Usage"><span> The script will: Loading @@ -146,6 +156,64 @@ Please note that this script alters the barcode whitelist. Known iCELL8 barcodes ### Manual <span id="Help"><span> #### Locally instaleld manual You can display a manual from the locally installed universc directory with: ``` man man/launch_universc.sh ``` Note that the working directory must be `universc` or the full path to the man directory must be given. #### Installing the manual with root priviliges: The manual can be installed as follows on Mac and Linux. ``` # add manual directory to PATH if not already found ## check config for Linux if [[ -f /etc/manpath.config ]] then CONFIG="/etc/manpath.config" fi ## check config for Mac if [[ -f /etc/manpaths ]] then CONFIG="/etc/manpaths" fi if [[ ! -z $CONFIG ]] then MANDIR=`tail -n 1 ${CONFIG}` else if [[ ! -z $MANPATH ]] then SHELL_RC=`echo ~/.${0}rc` echo "export MANPATH=/usr/local/man" >> $SHELL_RC MANDIR=`echo ${MANPATH} | cut -d: -f1` fi fi sudo mkdir -p ${MANDIR}/man1 cp man/launch_universc.sh man/launch_universc.sh.1 sudo mv man/launch_universc.sh.1 ${MANDIR}/man1/launch_universc.sh.1 gzip ${MANDIR}/man1/launch_universc.sh.1 ``` Alternatively the man can be installed with: ``` cp man/launch_universc.sh man/launch_universc.sh.1 sudo install -g 0 -o 0 -m 0644 man/launch_universc.sh.1 ${MANDIR}/man1 ``` The manual can then be called from any directory as follows: ``` man launch_universc.sh ``` ` -> change to make? #### Help menu You can access the following help menu with `launch_universc.sh --help` in the terminal. ``` Usage: bash launch_universc.sh --testrun -t THECHNOLOGY Loading Loading @@ -245,3 +313,4 @@ data generated from other platforms. Therefore 'launch_universc.sh' does not support Cloupe files and you should not use them with technologies other than 10x Genomics. man/convert.sh 100644 → 100755 +0 −0 File mode changed from 100644 to 100755. View file Loading
README.md +69 −0 Original line number Diff line number Diff line Loading @@ -120,6 +120,16 @@ This script will run in bash on any OS (but it has only been tested on Linux Deb with this configuration requires a lot of memory (40Gb) so running on server is recommended. SGE job modes are supported to run cellranger with multiple threads. -> migrate to Makefile? ### System Requirements ...Unix systems with cellranger installed. ### Docker image ... ## Usage <span id="Usage"><span> The script will: Loading @@ -146,6 +156,64 @@ Please note that this script alters the barcode whitelist. Known iCELL8 barcodes ### Manual <span id="Help"><span> #### Locally instaleld manual You can display a manual from the locally installed universc directory with: ``` man man/launch_universc.sh ``` Note that the working directory must be `universc` or the full path to the man directory must be given. #### Installing the manual with root priviliges: The manual can be installed as follows on Mac and Linux. ``` # add manual directory to PATH if not already found ## check config for Linux if [[ -f /etc/manpath.config ]] then CONFIG="/etc/manpath.config" fi ## check config for Mac if [[ -f /etc/manpaths ]] then CONFIG="/etc/manpaths" fi if [[ ! -z $CONFIG ]] then MANDIR=`tail -n 1 ${CONFIG}` else if [[ ! -z $MANPATH ]] then SHELL_RC=`echo ~/.${0}rc` echo "export MANPATH=/usr/local/man" >> $SHELL_RC MANDIR=`echo ${MANPATH} | cut -d: -f1` fi fi sudo mkdir -p ${MANDIR}/man1 cp man/launch_universc.sh man/launch_universc.sh.1 sudo mv man/launch_universc.sh.1 ${MANDIR}/man1/launch_universc.sh.1 gzip ${MANDIR}/man1/launch_universc.sh.1 ``` Alternatively the man can be installed with: ``` cp man/launch_universc.sh man/launch_universc.sh.1 sudo install -g 0 -o 0 -m 0644 man/launch_universc.sh.1 ${MANDIR}/man1 ``` The manual can then be called from any directory as follows: ``` man launch_universc.sh ``` ` -> change to make? #### Help menu You can access the following help menu with `launch_universc.sh --help` in the terminal. ``` Usage: bash launch_universc.sh --testrun -t THECHNOLOGY Loading Loading @@ -245,3 +313,4 @@ data generated from other platforms. Therefore 'launch_universc.sh' does not support Cloupe files and you should not use them with technologies other than 10x Genomics.
