From 79abc87410ab0baa0a7284efa908a056a6f042bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jul 2024 12:02:48 +0200 Subject: [PATCH 1/2] copy missing rsem_perl_utils.pm in DETONATE, since it's required by rsem-eval-calculate-score command --- .../easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index c1457cc041c..63246fc43ac 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -45,16 +45,20 @@ buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -fopenmp" && cd ../rsem-eval && make runtest = 'test' -files_to_copy = [(['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*'], 'bin')] +files_to_copy = [ + (['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*', '../rsem-eval/*.pm'], 'bin'), +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ref-eval', 'ref-eval-estimate-true-assembly', 'rsem-build-read-index', 'rsem-eval-calculate-score', 'rsem-eval-estimate-transcript-length-distribution', 'rsem-eval-run-em', 'rsem-extract-reference-transcripts', - 'rsem-parse-alignments', 'rsem-plot-model', 'rsem-preref', 'rsem-sam-validator', - 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', + 'rsem-parse-alignments', 'rsem_perl_utils.pm', 'rsem-plot-model', 'rsem-preref', + 'rsem-sam-validator', 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', 'rsem-synthesis-reference-transcripts']], 'dirs': [], } +sanity_check_commands = [r"rsem-eval-calculate-score --help 2>&1 | grep 'rsem-eval-calculate-score \[options\]'"] + moduleclass = 'bio' From 30c7c9c502fb943271fe1100fa21b4ad9794969e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Sep 2024 18:15:42 +0200 Subject: [PATCH 2/2] add missing Perl dependency for DETONATE v1.11 --- easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index 63246fc43ac..24a8b13835c 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -33,6 +33,7 @@ builddependencies = [ ] dependencies = [ + ('Perl', '5.36.1'), ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), ('BamTools', '2.5.2'),