From d3b6b07abe984d7cab50e3990bda444fdaafd26a Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 31 Jul 2024 13:08:36 +1200 Subject: [PATCH 1/3] Added echo for debug on mmc --- modules/local/assemblathon_stats.nf | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/modules/local/assemblathon_stats.nf b/modules/local/assemblathon_stats.nf index 3ef37de5..172ffd45 100644 --- a/modules/local/assemblathon_stats.nf +++ b/modules/local/assemblathon_stats.nf @@ -21,6 +21,9 @@ process ASSEMBLATHON_STATS { script: def VERSION = "github/PlantandFoodResearch/assemblathon2-analysis/a93cba2" """ + echo "Echo PATH..." + echo \$PATH + paths_to_check=\$(printf "%s\\n" \$(echo \$PATH | tr ':' ' ') \\ | xargs -I {} find {} -maxdepth 0 -print 2>/dev/null \\ | grep -v '^\$' \\ @@ -28,8 +31,14 @@ process ASSEMBLATHON_STATS { | xargs ) + echo "Echo paths_to_check..." + echo \$paths_to_check + falite_path="\$(find \$paths_to_check -name FAlite_a93cba2.pm)" + echo "Echo falite_path..." + echo \$falite_path + ln -s "\$falite_path" FAlite_a93cba2.pm PERL5LIB=./ assemblathon_stats_a93cba2.pl \\ From c697d3b3d6c30eba97a3ac3d2eca20f420d86ff1 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 31 Jul 2024 14:00:22 +1200 Subject: [PATCH 2/3] Now using the first result from find to link FAlite --- modules/local/assemblathon_stats.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/assemblathon_stats.nf b/modules/local/assemblathon_stats.nf index 172ffd45..5057096a 100644 --- a/modules/local/assemblathon_stats.nf +++ b/modules/local/assemblathon_stats.nf @@ -34,7 +34,7 @@ process ASSEMBLATHON_STATS { echo "Echo paths_to_check..." echo \$paths_to_check - falite_path="\$(find \$paths_to_check -name FAlite_a93cba2.pm)" + falite_path="\$(find \$paths_to_check -name FAlite_a93cba2.pm | head -n 1)" echo "Echo falite_path..." echo \$falite_path From 4e86875ec2650199245290ffee9b5e3e90a2c0a5 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 31 Jul 2024 15:04:41 +1200 Subject: [PATCH 3/3] Fixed multiple bin binds failure in ASSEMBLATHON_STATS --- CHANGELOG.md | 5 +++-- modules/local/assemblathon_stats.nf | 9 --------- 2 files changed, 3 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2618b3b1..2d3e0081 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,8 +24,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 5. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly does not contain any LTRs [#92](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/92) 6. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly is not writable [#98](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/98) 7. Now soft masked regions are unmasked before computing LAI [#117](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/117) -8. Changed `NextFlow` to `Nextflow` -9. Updated citation to Bioinformatics +8. Fixed a bug in `ASSEMBLATHON_STATS` which caused it to fail on MMC executor due to multiple binds of the `bin` directory +9. Changed `NextFlow` to `Nextflow` +10. Updated citation to Bioinformatics ### `Dependencies` diff --git a/modules/local/assemblathon_stats.nf b/modules/local/assemblathon_stats.nf index 5057096a..363a0e21 100644 --- a/modules/local/assemblathon_stats.nf +++ b/modules/local/assemblathon_stats.nf @@ -21,9 +21,6 @@ process ASSEMBLATHON_STATS { script: def VERSION = "github/PlantandFoodResearch/assemblathon2-analysis/a93cba2" """ - echo "Echo PATH..." - echo \$PATH - paths_to_check=\$(printf "%s\\n" \$(echo \$PATH | tr ':' ' ') \\ | xargs -I {} find {} -maxdepth 0 -print 2>/dev/null \\ | grep -v '^\$' \\ @@ -31,14 +28,8 @@ process ASSEMBLATHON_STATS { | xargs ) - echo "Echo paths_to_check..." - echo \$paths_to_check - falite_path="\$(find \$paths_to_check -name FAlite_a93cba2.pm | head -n 1)" - echo "Echo falite_path..." - echo \$falite_path - ln -s "\$falite_path" FAlite_a93cba2.pm PERL5LIB=./ assemblathon_stats_a93cba2.pl \\