From 827130d38566add7f3283f5013afa62235a03e6e Mon Sep 17 00:00:00 2001 From: Aaron Kolbecher Date: Mon, 21 Oct 2024 11:06:05 +0200 Subject: [PATCH 1/4] Added irma recipe for version 1.1.4 --- recipes/irma/irma-check-dir-writable.patch | 12 ++++---- recipes/irma/irma-fix-bin-cmds.patch | 33 +++++++++++----------- recipes/irma/meta.yaml | 4 +-- 3 files changed, 24 insertions(+), 25 deletions(-) diff --git a/recipes/irma/irma-check-dir-writable.patch b/recipes/irma/irma-check-dir-writable.patch index 57996031884e8..38e8cbeeb026f 100644 --- a/recipes/irma/irma-check-dir-writable.patch +++ b/recipes/irma/irma-check-dir-writable.patch @@ -1,11 +1,11 @@ ---- IRMA 2022-05-09 15:15:26.345377197 -0500 -+++ IRMA 2022-05-09 15:19:18.818708355 -0500 -@@ -111,7 +111,7 @@ +--- IRMA 2024-02-21 18:55:07.000000000 +0100 ++++ IRMA 2024-10-21 10:37:13.744040564 +0200 +@@ -141,7 +141,7 @@ # make sure output directory is valid - if [ ! -w "$destination_directory" ];then -- abort "output directory not writable: $destination_directory" -+ timestamp "WARNING: output directory may not be writable: $destination_directory" + if [ ! -w "$destination_directory" ]; then +- abort "output directory not writable: $destination_directory" ++ timestamp "WARNING: output directory may not writable: $destination_directory" fi # test input files diff --git a/recipes/irma/irma-fix-bin-cmds.patch b/recipes/irma/irma-fix-bin-cmds.patch index 6e85b5d064f08..59e46b5a22c91 100644 --- a/recipes/irma/irma-fix-bin-cmds.patch +++ b/recipes/irma/irma-fix-bin-cmds.patch @@ -1,6 +1,6 @@ ---- IRMA 2021-03-11 13:45:41.000000000 -0600 -+++ IRMA 2021-06-04 16:18:36.088939674 -0500 -@@ -140,14 +140,14 @@ +--- IRMA 2024-02-21 18:55:07.000000000 +0100 ++++ IRMA 2024-10-21 10:52:21.634249943 +0200 +@@ -172,14 +172,14 @@ check_prgm Rscript check_prgm perl @@ -18,14 +18,13 @@ -BASH=bash +RSCRIPT="Rscript" +BASH="bash" + MERGESAMPAIRS=("$spath/mergeSAMpairs.pl") + FASTQ_CONVERTER=("$spath/fastQ_converter.pl") - # select cat for reading reads - if [ "${#LEFT}" -gt "2" ];then -@@ -204,14 +204,19 @@ - exit 0 - fi +@@ -267,14 +267,18 @@ + fi fi -+ + +if [ -r "./irma_config.sh" ]; then + echo "Loading config file 'irma_config.sh'" + source "./irma_config.sh" @@ -33,15 +32,15 @@ + echo "No user config file 'irma_config.sh' specified." +fi + - [ ! -z "$LFASTM" ] && SECONDARY_SORT=$LFASTM + [ -n "$LFASTM" ] && SECONDARY_SORT=$LFASTM REF1_SET=$REF_SET # selection of zip utility --if command -v "$spath"/pigz_$OS >/dev/null 2>&1;then -- ZIP="$spath"/pigz_$OS -- Z_OPTS="-p $DOUBLE_LOCAL_PROC -4" --elif command -v pigz >/dev/null 2>&1;then +-if command -v "$spath"/pigz_$OS > /dev/null 2>&1; then +- ZIP="$spath"/pigz_$OS +- Z_OPTS="-p $DOUBLE_LOCAL_PROC -4" +-elif command -v pigz > /dev/null 2>&1; then +if command -v "pigz" >/dev/null 2>&1;then - ZIP="pigz" - Z_OPTS="-p $DOUBLE_LOCAL_PROC -4" - elif command -v gzip >/dev/null 2>&1;then + ZIP="pigz" + Z_OPTS="-p $DOUBLE_LOCAL_PROC -4" + elif command -v gzip > /dev/null 2>&1; then diff --git a/recipes/irma/meta.yaml b/recipes/irma/meta.yaml index 3e1a180a3615e..8f8eaeb477d45 100644 --- a/recipes/irma/meta.yaml +++ b/recipes/irma/meta.yaml @@ -1,5 +1,5 @@ {% set name = "IRMA" %} -{% set version = "1.0.3" %} +{% set version = "1.1.4" %} {% set hash_type = "sha256" %} {% set hash_value = "c5f6b452e1a6cfa8dcb02d1646c9e30e071557327a7cf11cab91a9b92e0eb455" %} @@ -8,7 +8,7 @@ package: version: {{ version }} source: - url: https://wonder.cdc.gov/amd/flu/irma/flu-amd-202209.zip + url: https://wonder.cdc.gov/amd/flu/irma/flu-amd-202402.zip {{ hash_type }}: {{ hash_value }} patches: - irma-fix-bin-cmds.patch From 5871acab681233ccf686767a9f5262e9de5b70fb Mon Sep 17 00:00:00 2001 From: Aaron Kolbecher Date: Mon, 21 Oct 2024 12:23:08 +0200 Subject: [PATCH 2/4] Corrected hash value --- recipes/irma/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/irma/meta.yaml b/recipes/irma/meta.yaml index 8f8eaeb477d45..4984830db69c0 100644 --- a/recipes/irma/meta.yaml +++ b/recipes/irma/meta.yaml @@ -1,7 +1,7 @@ {% set name = "IRMA" %} {% set version = "1.1.4" %} {% set hash_type = "sha256" %} -{% set hash_value = "c5f6b452e1a6cfa8dcb02d1646c9e30e071557327a7cf11cab91a9b92e0eb455" %} +{% set hash_value = "483183c5d18a718df5efe2bf4411f80e026fd169247e5b5cb614cb2e9998425b" %} package: name: {{ name|lower }} From 0e139b9b1a95f12302b2d0b9710dd57ea5b1d594 Mon Sep 17 00:00:00 2001 From: Aaron Kolbecher Date: Mon, 21 Oct 2024 12:41:56 +0200 Subject: [PATCH 3/4] Added run_exports and removed hash variables --- recipes/irma/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/irma/meta.yaml b/recipes/irma/meta.yaml index 4984830db69c0..81d3c6a5a1b33 100644 --- a/recipes/irma/meta.yaml +++ b/recipes/irma/meta.yaml @@ -1,7 +1,5 @@ {% set name = "IRMA" %} {% set version = "1.1.4" %} -{% set hash_type = "sha256" %} -{% set hash_value = "483183c5d18a718df5efe2bf4411f80e026fd169247e5b5cb614cb2e9998425b" %} package: name: {{ name|lower }} @@ -9,7 +7,7 @@ package: source: url: https://wonder.cdc.gov/amd/flu/irma/flu-amd-202402.zip - {{ hash_type }}: {{ hash_value }} + sha256: 483183c5d18a718df5efe2bf4411f80e026fd169247e5b5cb614cb2e9998425b patches: - irma-fix-bin-cmds.patch - label-fix-bin-cmds.patch @@ -18,6 +16,8 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('irma', max_pin="x.x") }} requirements: host: From 9296983a1221cff32badb361e2dc9bdd98405f81 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Mon, 21 Oct 2024 13:44:56 +0200 Subject: [PATCH 4/4] Update recipes/irma/irma-check-dir-writable.patch --- recipes/irma/irma-check-dir-writable.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/irma/irma-check-dir-writable.patch b/recipes/irma/irma-check-dir-writable.patch index 38e8cbeeb026f..b6db1d5d61d46 100644 --- a/recipes/irma/irma-check-dir-writable.patch +++ b/recipes/irma/irma-check-dir-writable.patch @@ -5,7 +5,7 @@ # make sure output directory is valid if [ ! -w "$destination_directory" ]; then - abort "output directory not writable: $destination_directory" -+ timestamp "WARNING: output directory may not writable: $destination_directory" ++ timestamp "WARNING: output directory may not be writable: $destination_directory" fi # test input files