From d31643a7c88a6326891fabe20fa2b990c87af7fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Thu, 10 Nov 2022 13:43:08 +0100 Subject: [PATCH 1/9] Draft of the pipeline installation in EESSI --- EESSI-pilot-install-software.sh | 6 ++++++ eessi-2021.12.yml | 4 ++++ 2 files changed, 10 insertions(+) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index dc50f7fae2..399c70265e 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -362,6 +362,12 @@ fail_msg="Installation of Nextflow failed, that's unexpected..." $EB -r --from-pr 16531 Nextflow-22.10.1.eb check_exit_code $? "${ok_msg}" "${fail_msg}" +echo ">> Installing requirements for the https://nf-co.re/mag v2.2.1 pipeline..." +ok_msg="The full Nextflow pipeline is installed, the work must flow..." +fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..." +$EB --robot --from-pr 16577,16590,16589,16592,16591,16576 && $EB --robot AdapterRemoval-2.3.2-GCC-10.3.0.eb BCFtools-1.12-GCC-10.3.0.eb Bowtie2-2.4.4-GCC-10.3.0.eb BUSCO-5.4.2-foss-2021a.eb fastp-0.23.2-GCC-10.3.0.eb FastQC-0.11.9-Java-11.eb GTDB-Tk-2.0.0-foss-2021a.eb Kraken2-2.1.2-gompi-2021a.eb KronaTools-2.8-GCC-10.3.0.eb MultiQC-1.11-foss-2021a.eb prodigal-2.6.3-GCCcore-10.3.0.eb prokka-1.14.5-gompi-2021a.eb QUAST-5.0.2-foss-2021a.eb SPAdes-3.15.3-GCC-10.3.0.eb +check_exit_code $? "${ok_msg}" "${fail_msg}" + ### add packages here echo ">> Creating/updating Lmod cache..." diff --git a/eessi-2021.12.yml b/eessi-2021.12.yml index 58101777ca..0d85b5e3db 100644 --- a/eessi-2021.12.yml +++ b/eessi-2021.12.yml @@ -57,3 +57,7 @@ software: toolchains: SYSTEM: versions: '22.10.1' + Nextflow-mag-pipeline: + toolchains: + foss-2021a: + versions: '2.2.1' From 21b69808d4c51121520effe4600ce9752069fd3d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Thu, 10 Nov 2022 17:05:41 +0100 Subject: [PATCH 2/9] Update the Nextflow-pipeline PR --- EESSI-pilot-install-software.sh | 4 ++-- eessi-2021.12.yml | 6 ++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index 399c70265e..23d99a77b5 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -362,10 +362,10 @@ fail_msg="Installation of Nextflow failed, that's unexpected..." $EB -r --from-pr 16531 Nextflow-22.10.1.eb check_exit_code $? "${ok_msg}" "${fail_msg}" -echo ">> Installing requirements for the https://nf-co.re/mag v2.2.1 pipeline..." +echo ">> Installing requirements for the Nextflow mag 20221110 pipeline..." ok_msg="The full Nextflow pipeline is installed, the work must flow..." fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..." -$EB --robot --from-pr 16577,16590,16589,16592,16591,16576 && $EB --robot AdapterRemoval-2.3.2-GCC-10.3.0.eb BCFtools-1.12-GCC-10.3.0.eb Bowtie2-2.4.4-GCC-10.3.0.eb BUSCO-5.4.2-foss-2021a.eb fastp-0.23.2-GCC-10.3.0.eb FastQC-0.11.9-Java-11.eb GTDB-Tk-2.0.0-foss-2021a.eb Kraken2-2.1.2-gompi-2021a.eb KronaTools-2.8-GCC-10.3.0.eb MultiQC-1.11-foss-2021a.eb prodigal-2.6.3-GCCcore-10.3.0.eb prokka-1.14.5-gompi-2021a.eb QUAST-5.0.2-foss-2021a.eb SPAdes-3.15.3-GCC-10.3.0.eb +$EB --robot --from-pr 16576,16577,16589,16590,16591,16592,16612,16613 check_exit_code $? "${ok_msg}" "${fail_msg}" ### add packages here diff --git a/eessi-2021.12.yml b/eessi-2021.12.yml index 0d85b5e3db..e7335588aa 100644 --- a/eessi-2021.12.yml +++ b/eessi-2021.12.yml @@ -57,7 +57,9 @@ software: toolchains: SYSTEM: versions: '22.10.1' - Nextflow-mag-pipeline: + Nextflow-pipeline: toolchains: foss-2021a: - versions: '2.2.1' + versions: + '20221110' + versionsuffix: -mag From 7eeacc998a485f4cf32436fc1605b6a2ef1fb64a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Fri, 11 Nov 2022 09:35:46 +0100 Subject: [PATCH 3/9] Update Nextflow pipeline name --- eessi-2021.12.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/eessi-2021.12.yml b/eessi-2021.12.yml index e7335588aa..4ebaeb94d9 100644 --- a/eessi-2021.12.yml +++ b/eessi-2021.12.yml @@ -57,9 +57,7 @@ software: toolchains: SYSTEM: versions: '22.10.1' - Nextflow-pipeline: + nf-core-mag: toolchains: foss-2021a: - versions: - '20221110' - versionsuffix: -mag + versions: '20221110' From e0ec46cefebc1bce90235a9986bdf5a43f1f30b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Fri, 11 Nov 2022 11:03:33 +0100 Subject: [PATCH 4/9] Add new PRs --- EESSI-pilot-install-software.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index 23d99a77b5..7a75efc054 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -365,7 +365,7 @@ check_exit_code $? "${ok_msg}" "${fail_msg}" echo ">> Installing requirements for the Nextflow mag 20221110 pipeline..." ok_msg="The full Nextflow pipeline is installed, the work must flow..." fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..." -$EB --robot --from-pr 16576,16577,16589,16590,16591,16592,16612,16613 +$EB --robot --from-pr 16576,16577,16589,16590,16591,16592,16612,16613,16615,16617 check_exit_code $? "${ok_msg}" "${fail_msg}" ### add packages here From fb934d4ebb034122d8aac9334389e90ac740c4db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Tue, 15 Nov 2022 18:00:26 +0100 Subject: [PATCH 5/9] Fix the list of PR to only the bundle and the MetaBAT fix --- EESSI-pilot-install-software.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index 7a75efc054..ecfb2dc4eb 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -365,7 +365,7 @@ check_exit_code $? "${ok_msg}" "${fail_msg}" echo ">> Installing requirements for the Nextflow mag 20221110 pipeline..." ok_msg="The full Nextflow pipeline is installed, the work must flow..." fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..." -$EB --robot --from-pr 16576,16577,16589,16590,16591,16592,16612,16613,16615,16617 +$EB --from-pr 16624 MetaBAT-2.15-gompi-2021a.eb -r && $EB --from-pr 16613 -r check_exit_code $? "${ok_msg}" "${fail_msg}" ### add packages here From 85ea3cddcc298e3a99ab3d6d823212a8b779fcb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Wed, 14 Dec 2022 14:32:07 +0100 Subject: [PATCH 6/9] Install R-4.1.0-foss-2021a.eb first for the Nextflow mag pipeline to make sure all SHA256 checksums for extensions are correct AND to speed up the installation with --parallel-extensions-install --- EESSI-pilot-install-software.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index ecfb2dc4eb..6a11802f31 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -365,7 +365,7 @@ check_exit_code $? "${ok_msg}" "${fail_msg}" echo ">> Installing requirements for the Nextflow mag 20221110 pipeline..." ok_msg="The full Nextflow pipeline is installed, the work must flow..." fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..." -$EB --from-pr 16624 MetaBAT-2.15-gompi-2021a.eb -r && $EB --from-pr 16613 -r +$EB --from-pr 14987 R-4.1.0-foss-2021a.eb -r --parallel-extensions-install --experimental && $EB --from-pr 16624 MetaBAT-2.15-gompi-2021a.eb -r && $EB --from-pr 16613 -r check_exit_code $? "${ok_msg}" "${fail_msg}" ### add packages here From aeab8e0392c317bc7a214974b3a57b8f5782abdc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Wed, 14 Dec 2022 14:36:28 +0100 Subject: [PATCH 7/9] Use the last R-4.1.0-foss-2021a.eb PR to use SYSTEM template constant instead of True in dependencies --- EESSI-pilot-install-software.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index 6a11802f31..33ae855c65 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -365,7 +365,7 @@ check_exit_code $? "${ok_msg}" "${fail_msg}" echo ">> Installing requirements for the Nextflow mag 20221110 pipeline..." ok_msg="The full Nextflow pipeline is installed, the work must flow..." fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..." -$EB --from-pr 14987 R-4.1.0-foss-2021a.eb -r --parallel-extensions-install --experimental && $EB --from-pr 16624 MetaBAT-2.15-gompi-2021a.eb -r && $EB --from-pr 16613 -r +$EB --from-pr 16386 R-4.1.0-foss-2021a.eb -r --parallel-extensions-install --experimental && $EB --from-pr 16624 MetaBAT-2.15-gompi-2021a.eb -r && $EB --from-pr 16613 -r check_exit_code $? "${ok_msg}" "${fail_msg}" ### add packages here From 6243c5deadea3360108d1c060300c8bd0ef48ae7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Wed, 14 Dec 2022 16:14:36 +0100 Subject: [PATCH 8/9] Add R 4.1.0 as a separate PR in the EESSI pilot script --- EESSI-pilot-install-software.sh | 8 +++++++- eessi-2021.12.yml | 4 ++++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index 33ae855c65..cee9e137cc 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -362,10 +362,16 @@ fail_msg="Installation of Nextflow failed, that's unexpected..." $EB -r --from-pr 16531 Nextflow-22.10.1.eb check_exit_code $? "${ok_msg}" "${fail_msg}" +echo ">> Installing R 4.1.0 (better be patient)..." +ok_msg="R installed, wow!" +fail_msg="Installation of R failed, so sad..." +$EB --from-pr 16386 R-4.1.0-foss-2021a.eb --robot --parallel-extensions-install --experimental +check_exit_code $? "${ok_msg}" "${fail_msg}" + echo ">> Installing requirements for the Nextflow mag 20221110 pipeline..." ok_msg="The full Nextflow pipeline is installed, the work must flow..." fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..." -$EB --from-pr 16386 R-4.1.0-foss-2021a.eb -r --parallel-extensions-install --experimental && $EB --from-pr 16624 MetaBAT-2.15-gompi-2021a.eb -r && $EB --from-pr 16613 -r +$EB --from-pr 16624 MetaBAT-2.15-gompi-2021a.eb -r && $EB --from-pr 16613 -r check_exit_code $? "${ok_msg}" "${fail_msg}" ### add packages here diff --git a/eessi-2021.12.yml b/eessi-2021.12.yml index 4ebaeb94d9..04cfd5dc69 100644 --- a/eessi-2021.12.yml +++ b/eessi-2021.12.yml @@ -53,6 +53,10 @@ software: versions: '3.9.1.1': versionsuffix: -dmpar + R: + toolchains: + foss-2021a: + versions: '4.1.0' Nextflow: toolchains: SYSTEM: From 513c8962542326369323badb019b436696c82426 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Moretti?= Date: Wed, 14 Dec 2022 16:23:18 +0100 Subject: [PATCH 9/9] Move R 4.1.0 in a separate PR --- EESSI-pilot-install-software.sh | 6 ------ eessi-2021.12.yml | 4 ---- 2 files changed, 10 deletions(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index cee9e137cc..ecfb2dc4eb 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -362,12 +362,6 @@ fail_msg="Installation of Nextflow failed, that's unexpected..." $EB -r --from-pr 16531 Nextflow-22.10.1.eb check_exit_code $? "${ok_msg}" "${fail_msg}" -echo ">> Installing R 4.1.0 (better be patient)..." -ok_msg="R installed, wow!" -fail_msg="Installation of R failed, so sad..." -$EB --from-pr 16386 R-4.1.0-foss-2021a.eb --robot --parallel-extensions-install --experimental -check_exit_code $? "${ok_msg}" "${fail_msg}" - echo ">> Installing requirements for the Nextflow mag 20221110 pipeline..." ok_msg="The full Nextflow pipeline is installed, the work must flow..." fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..." diff --git a/eessi-2021.12.yml b/eessi-2021.12.yml index 04cfd5dc69..4ebaeb94d9 100644 --- a/eessi-2021.12.yml +++ b/eessi-2021.12.yml @@ -53,10 +53,6 @@ software: versions: '3.9.1.1': versionsuffix: -dmpar - R: - toolchains: - foss-2021a: - versions: '4.1.0' Nextflow: toolchains: SYSTEM: