diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py index a7eacb33806c..8f62617e45a3 100644 --- a/lib/galaxy/tool_util/deps/mulled/util.py +++ b/lib/galaxy/tool_util/deps/mulled/util.py @@ -335,7 +335,14 @@ def v2_image_name( >>> multi_targets_versionless = [build_target("samtools"), build_target("bwa")] >>> v2_image_name(multi_targets_versionless) 'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40' + >>> targets_version_with_build = [build_target("samtools", version="1.3.1=h9071d68_10"), build_target("bedtools", version="2.26.0=0")] + >>> v2_image_name(targets_version_with_build) + 'mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:8e86df67d257ce6494ae12b2c60e1b94025ea529' + >>> targets_version_with_build = [build_target("samtools", version="1.3.1", build="h9071d68_10"), build_target("bedtools", version="2.26.0", build="0")] + >>> v2_image_name(targets_version_with_build) + 'mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619' """ + if name_override is not None: print( "WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result." diff --git a/test/functional/tools/mulled_example_multi_2.xml b/test/functional/tools/mulled_example_multi_2.xml new file mode 100644 index 000000000000..5347dace94b7 --- /dev/null +++ b/test/functional/tools/mulled_example_multi_2.xml @@ -0,0 +1,79 @@ + + + + bedtools + samtools + + + + + + + samtools + bedtools + + '$out_file1' && +echo "Moo" >> '$out_file1' && +samtools >> '$out_file1' 2>&1 && +echo "Cow" >> '$out_file1' && + +touch "\${TMP:-/tmp}/job_tmp" && +touch "\${TEMP:-/tmp}/job_temp" && +touch "\${TMPDIR:-/tmp}/job_tmpdir" + ]]> + + + + + + + + + + + 10.1093/bioinformatics/btq033 + + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/},} + + 10.1093/bioinformatics/btp352 + 10.1093/bioinformatics/btr076 + 10.1093/bioinformatics/btr509 + + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + + + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + + + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + + + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + + + diff --git a/test/integration/test_container_resolvers.py b/test/integration/test_container_resolvers.py index 2188cf3f9bb2..4f9f31f38edd 100644 --- a/test/integration/test_container_resolvers.py +++ b/test/integration/test_container_resolvers.py @@ -480,6 +480,11 @@ class MulledTestCase: mulled_hash = "mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619-0" +class MulledTestCaseWithBuildInfo: + tool_id = "mulled_example_multi_2" + mulled_hash = "mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:8e86df67d257ce6494ae12b2c60e1b94025ea529-0" + + class TestDefaultContainerResolvers(DockerContainerResolverTestCase, ContainerResolverTestCases, MulledTestCase): """ Test default container resolvers