diff --git a/cellranger/8.0.1/.gitignore b/cellranger/8.0.1/.gitignore new file mode 100755 index 0000000..3e25afe --- /dev/null +++ b/cellranger/8.0.1/.gitignore @@ -0,0 +1 @@ +cellranger-8.0.1 diff --git a/cellranger/8.0.1/README.md b/cellranger/8.0.1/README.md new file mode 100755 index 0000000..fe2d3f1 --- /dev/null +++ b/cellranger/8.0.1/README.md @@ -0,0 +1,52 @@ +# Installation + +```bash +## Commands used for installing the software +# Note: this uses a temporary download link generated after entering some +# information and agreeing to terms of use +curl -o cellranger-8.0.1.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-8.0.1.tar.gz?Expires=1729826286&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=NEDneyCsgwNbl7-d5rYnv77NveZxVXvBUdiDk6Po7EsaRGuqQQNGRXyEOEh3dwgy3z0B3rMPjHb8dof5i4EraOlfdfIy~qzC0n2VsS01xmw7iAVTsNyFvVj5bFKBIZa47xOEJRg7hwj3aUL1E2pgzF2zLIOlARcwvw~w8CGydz2PrVZBOBXt9yAkqgFUwuNZaDaMB7BmRwD75x14ZhfbzS6qHQQw40zmpSxgWm2h8mbBAEK6dwu7CMdfnT8f0rVuAlYRgkVQyvKLgNWgxDkB6VbGyVMyoflrklR98a-VAUd5kirV1~XnP0kBxmAyPpzXgB0y0zGaddacrZqgPUN~sg__" +tar -xzf cellranger-8.0.1.tar.gz +rm cellranger-8.0.1.tar.gz + +# A 10x-compatible reference genome is also required, and we install these as +# needed from here: +# +# https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +# +# into /dcs04/lieber/lcolladotor/annotationFiles_LIBD001/10x. + +## Ignore all downloaded/installed files +echo "cellranger-8.0.1" > .gitignore +chmod -R 775 . + +## Version control files +git add .gitignore +git add README.md +``` + +# Reproducibility + +```bash +## Evaluate the following commands +module list +date +echo "User: ${USER}" +echo "Hostname: ${HOSTNAME}" +``` + +```bash +## copy paste the output from the previous commands +$ module list + +Currently Loaded Modules: + 1) JHPCE_ROCKY9_DEFAULT_ENV 2) JHPCE_tools/3.0 + + + +$ date +Thu Oct 24 11:20:25 AM EDT 2024 +$ echo "User: ${USER}" +User: neagles +$ echo "Hostname: ${HOSTNAME}" +Hostname: compute-162.cm.cluster +```