From ff580bd1eaf6944babfda368fdd8babc6964a436 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 29 Oct 2024 11:50:55 +0000 Subject: [PATCH 1/6] add arm support for controlfreec --- recipes/control-freec/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/control-freec/meta.yaml b/recipes/control-freec/meta.yaml index fd4a71251279d..47395f7964145 100644 --- a/recipes/control-freec/meta.yaml +++ b/recipes/control-freec/meta.yaml @@ -50,3 +50,5 @@ extra: command line as well. identifiers: - biotools:freec + additional-platforms: + - linux-aarch64 From 722fc3e3b7e7a773c4701ddb198ea39d6952c331 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 29 Oct 2024 14:41:41 -0600 Subject: [PATCH 2/6] bump build --- recipes/control-freec/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/control-freec/meta.yaml b/recipes/control-freec/meta.yaml index 47395f7964145..312f1a1a2fc02 100644 --- a/recipes/control-freec/meta.yaml +++ b/recipes/control-freec/meta.yaml @@ -12,7 +12,7 @@ source: - perl_shebang.patch build: - number: 3 + number: 4 requirements: build: From f2749330f1ee225c199522b33e85e309ee9f1c8c Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 29 Oct 2024 17:19:52 -0500 Subject: [PATCH 3/6] Update meta.yaml --- recipes/control-freec/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/control-freec/meta.yaml b/recipes/control-freec/meta.yaml index 3f212e9307e8b..3fad42fb870be 100644 --- a/recipes/control-freec/meta.yaml +++ b/recipes/control-freec/meta.yaml @@ -14,7 +14,7 @@ source: - perl_shebang.patch build: - number: 4 + number: 1 run_exports: - {{ pin_subpackage('control-freec', max_pin="x") }} From 41fce3d570ca08064a314f52ced71c55b74d6fa8 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 30 Oct 2024 08:30:47 -0600 Subject: [PATCH 4/6] add debug to build.sh --- recipes/control-freec/build.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/control-freec/build.sh b/recipes/control-freec/build.sh index bfa671b9484e4..226e5371ee240 100644 --- a/recipes/control-freec/build.sh +++ b/recipes/control-freec/build.sh @@ -1,5 +1,6 @@ #!/bin/bash - +# Debug for ARM build, can remove later +set -x mkdir -p $PREFIX/bin From 97c23710f78aa3b7cc20a19e038401109ab740b8 Mon Sep 17 00:00:00 2001 From: David Lecomber Date: Mon, 11 Nov 2024 16:22:58 +0000 Subject: [PATCH 5/6] Replace 'which' with test -x to overcome path length issue in which for centos-7/8 --- recipes/control-freec/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/control-freec/meta.yaml b/recipes/control-freec/meta.yaml index 3fad42fb870be..806d4014eebe5 100644 --- a/recipes/control-freec/meta.yaml +++ b/recipes/control-freec/meta.yaml @@ -33,12 +33,12 @@ test: - freec - freec2bed.pl - freec2circos.pl - - which get_fasta_lengths.pl - - which makeGraph.R - - which makeGraph_Chromosome.R + - test -x ${PREFIX}/bin/get_fasta_lengths.pl + - test -x ${PREFIX}/bin/makeGraph.R + - test -x ${PREFIX}/bin/makeGraph_Chromosome.R - vcf2snpFreec.pl - - which assess_significance.R - - which makeGraph2.0.R + - test -x ${PREFIX}/bin/assess_significance.R + - test -x ${PREFIX}/bin/makeGraph2.0.R about: home: https://github.com/BoevaLab/FREEC From 97a3acb0bdc85df0b3aa22b032ff6fb4385e9add Mon Sep 17 00:00:00 2001 From: David Lecomber Date: Wed, 13 Nov 2024 09:48:35 +0000 Subject: [PATCH 6/6] * Add osx-arm64 to meta.yaml --- recipes/bioconductor-biobase/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml index f8f03fe0161a5..e2c3f05f7710c 100644 --- a/recipes/bioconductor-biobase/meta.yaml +++ b/recipes/bioconductor-biobase/meta.yaml @@ -42,6 +42,7 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - biotools:biobase