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clinical_strains_lpanamensis.yml
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clinical_strains_lpanamensis.yml
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Bootstrap: docker
From: debian:stable
## Order of sections:
## %labels: unknown, storing metadata
## %files: are before %post or installation procedures.
## %setup: in the host-system after base OS install.
## %post: in the container after base OS install.
## %test: run at end of build process.
## %environment: sourced at runtime, not build; if needed at build, do it in %post.
## %runscript: writes the container file /singularity and is run via 'singularity run'
%apphelp hpgltools_test
echo "Run the hpgltools test suite."
%apprun hpgltools_test
echo "Running the hpgltools test suite."
exec cd /data/hpgltools && make test
%environment
## If this works properly, I can delete the bashrc, apparently the contents of this stanza are
## written to /.singularity.d/env/90-environment.sh
## As of this writing, it appears VERSION is not propagated to the %post block, therefore
## the definition is repeated there.
. /usr/local/etc/bashrc
## Instead of copying files within the setup section, one should use the files block, I think because
## this is not run with elevated permissions.
%files
local/org.Lpanamensis.MHOMCOL81L13.v68.eg.db_2024.09.tar.gz /usr/local/org.Lpanamensis.MHOMCOL81L13.v68.eg.db_2024.09.tar.gz
local/BSGenome.Leishmania.panamensis.MHOMCOL81L13.v68_2024.09.tar.gz /usr/local/BSGenome.Leishmania.panamensis.MHOMCOL81L13.v68_2024.09.tar.gz
local/TxDb.Leishmania.panamensis.MHOMCOL81L13.TriTrypDB.v64_2023.07.tar.gz /usr/local/TxDb.Leishmania.panamensis.MHOMCOL81L13.TriTrypDB.v64_2023.07.tar.gz
local/etc/bashrc /usr/local/etc/bashrc
local/etc/deb_packages.txt /usr/local/etc/deb_packages.txt
local/etc/conda_packages.txt /usr/local/etc/conda_packages.txt
local/bin/bootstrap.R /usr/local/bin/bootstrap.R
local/bin/bootstrap.sh /usr/local/bin/bootstrap.sh
local/bin/runscript.sh /usr/local/bin/runscript.sh
data/Makefile /data/Makefile
data/renv.lock /data/renv.lock
data/renv/activate.R /data/renv/activate.R
data/renv/settings.json /data/renv/settings.json
data/renv/.gitignore /data/renv/.gitignore
local/etc/template /sw/modules/template
data/00preprocessing.Rmd /data/00preprocessing.Rmd
data/01datasets.Rmd /data/01datasets.Rmd
data/02pre_visualization.Rmd /data/02pre_visualization.Rmd
data/03differential_expression.Rmd /data/03differential_expression.Rmd
data/04post_visualization.Rmd /data/04post_visualization.Rmd
data/README.Rmd /data/README.Rmd
data/compare_strains/kmer_tree.Rmd /data/compare_strains/kmer_tree.Rmd
data/compare_strains/lbraziliensis_2904_v46.fasta.xz /data/compare_strains/lbraziliensis_2904_v46.fasta.xz
data/compare_strains/leishmania_guyanensis_202209.fasta.xz /data/compare_strains/leishmania_guyanensis_202209.fasta.xz
data/compare_strains/lpanamensis_cds.fasta.xz /data/compare_strains/lpanamensis_cds.fasta.xz
data/compare_strains/lpanamensis_col_zymodeme_genes.fasta.xz /data/compare_strains/lpanamensis_col_zymodeme_genes.fasta.xz
data/compare_strains/lpanamensis_psc1_v46.fasta.xz /data/compare_strains/lpanamensis_psc1_v46.fasta.xz
data/compare_strains/lpanamensis_v36.fasta.xz /data/compare_strains/lpanamensis_v36.fasta.xz
data/compare_strains/lpanamensis_v36.fasta.fai.xz /data/compare_strains/lpanamensis_v36.fasta.fai.xz
data/compare_strains/lpanamensis_z21_cds.fasta.xz /data/compare_strains/lpanamensis_z21_cds.fasta.xz
data/compare_strains/lpanamensis_z22_cds.fasta.xz /data/compare_strains/lpanamensis_z22_cds.fasta.xz
data/compare_strains/lpanamensis_z23_cds.fasta.xz /data/compare_strains/lpanamensis_z23_cds.fasta.xz
data/compare_strains/lpanamensis_z24_cds.fasta.xz /data/compare_strains/lpanamensis_z24_cds.fasta.xz
data/compare_strains/strain_12444_modified_z24.fasta.xz /data/compare_strains/strain_12444_modified_z24.fasta.xz
data/compare_strains/strain_12444_modified_z24.fasta.fai.xz /data/compare_strains/strain_12444_modified_z24.fasta.fai.xz
data/compare_strains/strain_2168_modified_z23.fasta.xz /data/compare_strains/strain_2168_modified_z23.fasta.xz
data/compare_strains/strain_2168_modified_z23.fasta.fai.xz /data/compare_strains/strain_2168_modified_z23.fasta.fai.xz
data/preprocessing/tmrc2_count_tables.tar /data/preprocessing/tmrc2_count_tables.tar
data/preprocessing/var_by_gene.tar /data/preprocessing/var_by_gene.tar
data/preprocessing/freebayes_tags.tar /data/preprocessing/freebayes_tags.tar
data/preprocessing/macrophage_host_counts.tar /data/preprocessing/macrophage_host_counts.tar
data/preprocessing/macrophage_parasite_counts.tar /data/preprocessing/macrophage_parasite_counts.tar
data/sample_sheets/ClinicalStrains_TMRC2.xlsx /data/sample_sheets/ClinicalStrains_TMRC2.xlsx
data/sample_sheets/tmrc2_macrophage_samples.xlsx /data/sample_sheets/tmrc2_macrophage_samples.xlsx
data/atb.bib /data/atb.bib
%help
String printed when "singularity help image.simg" is run.
%labels
Maintainer Ashton Trey Belew <[email protected]>
%post
echo "export CONTAINER_VERSION=202408" >> /versions.txt
echo "export BIOC_VERSION=3.19" >> /versions.txt
echo "export R_VERSION=4.4.1" >> /versions.txt
/usr/local/bin/bootstrap.sh
%runscript
/usr/local/bin/runscript.sh $*
## The setup block will be used to copy material which I cannot acquire
## automatically. Ideally this should only be a sample sheet and potentially
## count tables for now. ** NOTE ** This section is run as root! So be careful.
%setup
mkdir -p ${SINGULARITY_ROOTFS}/usr/local/bin
mkdir -p ${SINGULARITY_ROOTFS}/usr/local/etc
mkdir -p ${SINGULARITY_ROOTFS}/.emacs.d
mkdir -p ${SINGULARITY_ROOTFS}/data/compare_strains
mkdir -p ${SINGULARITY_ROOTFS}/data/preprocessing
mkdir -p ${SINGULARITY_ROOTFS}/data/renv
mkdir -p ${SINGULARITY_ROOTFS}/data/cpm
mkdir -p ${SINGULARITY_ROOTFS}/data/rpkm
mkdir -p ${SINGULARITY_ROOTFS}/data/images
mkdir -p ${SINGULARITY_ROOTFS}/data/figures
mkdir -p ${SINGULARITY_ROOTFS}/data/rda
mkdir -p ${SINGULARITY_ROOTFS}/data/excel
mkdir -p ${SINGULARITY_ROOTFS}/data/sample_sheets
mkdir -p ${SINGULARITY_ROOTFS}/output
mkdir -p ${SINGULARITY_ROOTFS}/sw/local/conda
mkdir -p ${SINGULARITY_ROOTFS}/sw/local/R/renv_cache
mkdir -p ${SINGULARITY_ROOTFS}/sw/modules
if test -e "${HOME}/hpgltools"; then
mkdir -p ${SINGULARITY_ROOTFS}/data/hpgltools && rsync -av "${HOME}/hpgltools/" "${SINGULARITY_ROOTFS}/data/hpgltools/"
else
mkdir -p ${SINGULARITY_ROOTFS}/data/hpgltools && git clone https://github.com/abelew/hpgltools "${SINGULARITY_ROOTFS}/data/hpgltools/"
fi
%test
echo "Making sure hpgltools got installed."
test -d "/data/hpgltools" || true