Changes between Version 13 and Version 14 of cypress/SingularityDockerhub

Timestamp:

03/27/2026 12:53:40 PM (4 months ago)

Author:

Carl Baribault

Comment:

Added detail to supply test data

cypress/SingularityDockerhub

@@ -63 +63 @@
 
 {{{
-singularity pull docker://r-base:latest  # creating .sif file takes ~6 minutes
+singularity pull docker://r-base:latest  # creating .sif file takes ~1 minute
 }}}
 
@@ -100 +100 @@
 }}}
 
-To run it with the minimum test dataset,
-Assuming the example dataset is extracted under /lustre/project/'''group/user'''/fastdtlmapper, where ''''group'''' is the group name and ''''user'''' is the user name,
+To download the minimum test dataset,
+
+{{{
+mkdir FastDTLmapper
+cd FastDTLmapper
+git init
+git remote add origin -f https://github.com/moshi4/FastDTLmapper.git
+git config core.sparseCheckout true
+echo "/example/minimum_dataset" > .git/info/sparse-checkout
+git pull origin main
+cd ..  # cd back to the parent folder
+}}}
+
+To run the example with the minimum test dataset,
+assuming the example dataset is extracted under /lustre/project/'''group/user'''/FastDTLmapper, where ''''group'''' is the group name and ''''user'''' is the user name (Note: If you encounter '''!FileNotFoundError''', be sure to change /home/'''user''' as well.),
 {{{
 export SINGULARITYENV_TMPDIR=/tmp
 export SINGULARITY_BINDPATH=/lustre/project/group/user:/home/user,$TMPDIR:/tmp
-singularity exec fastdtlmapper_latest.sif FastDTLmapper -i fastdtlmapper/example/minimum_dataset/fasta/ -t fastdtlmapper/example/minimum_dataset/species_tree.nwk -o fastdtlmapper/output_minimum
+singularity exec fastdtlmapper_latest.sif FastDTLmapper -i FastDTLmapper/example/minimum_dataset/fasta/ -t FastDTLmapper/example/minimum_dataset/species_tree.nwk -o FastDTLmapper/output_minimum
 }}}