From 290e3cbcb6a64e8716e9158d0e93bc1f137d676f Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Fri, 6 Oct 2023 21:26:54 +0200 Subject: [PATCH 1/6] {2023.06}[foss/2022a] add bio packages - set 2 --- eessi-2023.06-eb-4.8.1-2022a.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index b1bbe71da7..993f9db4d5 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -8,3 +8,10 @@ easyconfigs: - gzip-1.12-GCCcore-11.3.0.eb - lz4-1.9.3-GCCcore-11.3.0.eb - zstd-1.5.2-GCCcore-11.3.0.eb + - AdapterRemoval-2.3.3-GCC-11.3.0.eb + - BBMap-39.01-GCC-11.3.0.eb + - Beast-2.7.3-GCC-11.3.0.eb + - BEDTools-2.30.0-GCC-11.3.0.eb + - Bio-DB-HTS-3.01-GCC-11.3.0.eb + - Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb + - BWA-0.7.17-GCCcore-11.3.0.eb From 0a62656688dd14984fcb27f0185e86a9b1fec6e8 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Fri, 6 Oct 2023 22:46:02 +0200 Subject: [PATCH 2/6] removed BBMap because it failed to build --- eessi-2023.06-eb-4.8.1-2022a.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index 993f9db4d5..679b1c8092 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -9,7 +9,6 @@ easyconfigs: - lz4-1.9.3-GCCcore-11.3.0.eb - zstd-1.5.2-GCCcore-11.3.0.eb - AdapterRemoval-2.3.3-GCC-11.3.0.eb - - BBMap-39.01-GCC-11.3.0.eb - Beast-2.7.3-GCC-11.3.0.eb - BEDTools-2.30.0-GCC-11.3.0.eb - Bio-DB-HTS-3.01-GCC-11.3.0.eb From 5fcd337e2ce23c73c2b0a412b0ea179c08797c98 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sat, 7 Oct 2023 09:29:05 +0200 Subject: [PATCH 3/6] remove Beast (dependency Clang failed on aarch64) --- eessi-2023.06-eb-4.8.1-2022a.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index 679b1c8092..8e31b0ce23 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -9,7 +9,6 @@ easyconfigs: - lz4-1.9.3-GCCcore-11.3.0.eb - zstd-1.5.2-GCCcore-11.3.0.eb - AdapterRemoval-2.3.3-GCC-11.3.0.eb - - Beast-2.7.3-GCC-11.3.0.eb - BEDTools-2.30.0-GCC-11.3.0.eb - Bio-DB-HTS-3.01-GCC-11.3.0.eb - Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb From b48487dea43de4a79e9e7c9d001ff537318c895c Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sat, 7 Oct 2023 20:49:32 +0200 Subject: [PATCH 4/6] removed BWA, also fails on aarch64/generic --- eessi-2023.06-eb-4.8.1-2022a.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index 82a10ccba5..a76d41020d 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -17,4 +17,3 @@ easyconfigs: - NCO-5.1.0-foss-2022a.eb - AdapterRemoval-2.3.3-GCC-11.3.0.eb - BEDTools-2.30.0-GCC-11.3.0.eb - - BWA-0.7.17-GCCcore-11.3.0.eb From f3482bde4fc7aa07a765271372e7a44f9b02a379 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sat, 7 Oct 2023 21:05:28 +0200 Subject: [PATCH 5/6] {2023.06}[foss/2022a] add bio paackages - set 3 --- eessi-2023.06-eb-4.8.1-2022a.yml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index a09af3fe4b..677ff41958 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -15,3 +15,12 @@ easyconfigs: options: include-easyblocks-from-pr: 3012 - NCO-5.1.0-foss-2022a.eb + - Pysam-0.20.0-GCC-11.3.0.eb + - TransDecoder-5.5.0-GCC-11.3.0.eb + - VCFtools-0.1.16-GCC-11.3.0.eb + - VSEARCH-2.22.1-GCC-11.3.0.eb + - XML-LibXML-2.0207-GCCcore-11.3.0.eb + - CMake-3.24.3-GCCcore-11.3.0.eb + - elfutils-0.187-GCCcore-11.3.0.eb + - Ninja-1.10.2-GCCcore-11.3.0.eb + - Z3-4.10.2-GCCcore-11.3.0.eb From 335b63d396b5eaf40ebb56ab33d3a8b8e96cad82 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sat, 7 Oct 2023 21:43:23 +0200 Subject: [PATCH 6/6] removed VSEARCH, failed to build for all architectures --- eessi-2023.06-eb-4.8.1-2022a.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index 677ff41958..dc2377459d 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -18,7 +18,6 @@ easyconfigs: - Pysam-0.20.0-GCC-11.3.0.eb - TransDecoder-5.5.0-GCC-11.3.0.eb - VCFtools-0.1.16-GCC-11.3.0.eb - - VSEARCH-2.22.1-GCC-11.3.0.eb - XML-LibXML-2.0207-GCCcore-11.3.0.eb - CMake-3.24.3-GCCcore-11.3.0.eb - elfutils-0.187-GCCcore-11.3.0.eb