cure_fail_host_analyses.yml

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/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/ml_summary_tumaco_v1-v202408.xlsx /data/ml_summary_tumaco_v1-v202408.xlsx
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/preprocessing/pruned_counts_host.tar /data/preprocessing/pruned_counts_host.tar
data/preprocessing/pruned_counts_parasite.tar /data/preprocessing/pruned_counts_parasite.tar
data/preprocessing/scott_counts.tar /data/preprocessing/scott_counts.tar
data/sample_sheets/scott_sra_samples.xlsx /data/sample_sheets/scott_sra_samples.xlsx
data/sample_sheets/scott_capsule_studydesign.tsv /data/sample_sheets/scott_capsule_studydesign.tsv
data/sample_sheets/tmrc3_demographics.xlsx /data/sample_sheets/tmrc3_demographics.xlsx
data/sample_sheets/tmrc3_demographicsv2.xlsx /data/sample_sheets/tmrc3_demographicsv2.xlsx
data/sample_sheets/tmrc3_samples_pruned.xlsx /data/sample_sheets/tmrc3_samples_pruned.xlsx
data/sample_sheets/identified_parasite_species.xlsx /data/sample_sheets/identified_parasite_species.xlsx
data/sample_sheets/tmrc3_samples.xlsx /data/sample_sheets/tmrc3_samples.xlsx
data/Makefile /data/Makefile
data/README.Rmd /data/README.Rmd
data/00preprocessing.Rmd /data/00preprocessing.Rmd
data/01datasets.Rmd /data/01datasets.Rmd
data/02visualization.Rmd /data/02visualization.Rmd
data/03differential_expression_both.Rmd /data/03differential_expression_both.Rmd
data/04differential_expression_tumaco.Rmd /data/04differential_expression_tumaco.Rmd
data/05enrichment.Rmd /data/05enrichment.Rmd
data/06lrt_gsva.Rmd /data/06lrt_gsva.Rmd
data/07wgcna.Rmd /data/07wgcna.Rmd
data/08classifier_highvar.Rmd /data/08classifier_highvar.Rmd
data/atb.bib /data/atb.bib


%help
String printed when "singularity help image.simg" is run.


%labels
Maintainer Ashton Trey Belew <abelew@umd.edu>


%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
echo "export HPGLTOOLS_COMMIT='2ba131c696f93b44a2360e412fbba5b008699c83'" >> /versions.txt
/usr/local/bin/bootstrap.sh


%runscript
/usr/bin/time -f '\t%E real,\t%U user,\t%S sys,\t%K amem,\t%M mmem' /usr/local/bin/runscript.sh $*


## The setup block will be used to prepare material which I cannot acquire
## automatically.  Ideally this should just create some directories for the container.
##   ** 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/preprocessing
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


%test
echo "Making sure hpgltools got installed."
test -d "/data/hpgltools" || true