checking that cellranger has write-access

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.

- local install

##### Local install

- copy from root and add to PATH

If cellranger is not already installed we recommend installing it in a directory that

you have write access to such as `$HOME/local`.

#### Installing launch_universc.sh

##### Importing an installed version of cellranger

If cellranger has been installed by a system administrator, you will only have read-access

to that installation. You can still use rather than installing a new version but you

will need to copy it to your home directory and add this version to your PATH.

```

mkdir -p $HOME/local

cd ~/local

installed_version=$(echo $(which cellranger) | rev | cut -d"/" -f2- | rev)

cp -rv $installed_version  .

installed_directory=$(echo $(which cellranger) | rev | cut -d"/" -f2 | rev) 

cd $installed_directory

new_version=$(pwd)

#remove previous version from PATH

export PATH=$(echo $PATH |  sed "s;$installed_version:;;g")

#add new version to PATH

eval $(echo export PATH=$new_version:\$PATH)

cd ..

```

You should be able to see that the locally installed version can be called as follows:

```

echo $PATH

which cellranger

bash launch_universc.sh

```

#### Installing launch_universc.sh to the PATH

##### Running the script