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{tools}[system/system] Nextflow v24.10.2 #21939

Merged
merged 1 commit into from
Nov 29, 2024
Merged

{tools}[system/system] Nextflow v24.10.2 #21939

merged 1 commit into from
Nov 29, 2024
+36 −0

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pavelToman
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@pavelToman pavelToman commented Nov 29, 2024 •
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(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#457

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Updated software Nextflow-24.10.2.eb

Diff against Nextflow-24.04.4.eb

easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb

diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb
index c718972b66..75b0cb4a2d 100644
--- a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb
+++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb
@@ -1,7 +1,7 @@
 easyblock = 'Binary'
 
 name = 'Nextflow'
-version = '24.04.4'
+version = '24.10.2'
 
 homepage = 'https://www.nextflow.io/'
 description = """Nextflow is a reactive workflow framework and a programming DSL
@@ -10,26 +10,27 @@ description = """Nextflow is a reactive workflow framework and a programming DSL
 toolchain = SYSTEM
 
 source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/']
-sources = ['nextflow-%(version)s-all']
-checksums = ['9077cfb151d4bc8682f09a65a77f45346bf34dac5931e371dba0d51bf13a5076']
+sources = ['nextflow-%(version)s-dist']
+checksums = ['972bb4f4bcd30bb474c29c247ccf79289bbcd444f799f0307f61123e6b0f7475']
 
-dependencies = [('Java', '11')]
+dependencies = [('Java', '21')]
 
 install_cmds = [
     "mkdir -p %(installdir)s/bin",
-    "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin",
-    "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow",
-    "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-all",
+    "cp %(builddir)s/nextflow-%(version)s-dist %(installdir)s/bin",
+    "cd %(installdir)s/bin && ln -s nextflow-%(version)s-dist nextflow",
+    "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-dist",
 ]
 
 sanity_check_paths = {
-    'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'],
+    'files': ['bin/nextflow-%(version)s-dist', 'bin/nextflow'],
     'dirs': []
 }
 
 sanity_check_commands = [
     "nextflow -v",
     "nextflow help",
+    "nextflow info",
 ]
 
 moduleclass = 'tools'
Diff against Nextflow-24.04.2.eb

easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.2.eb

diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.2.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb
index 21a90e473c..75b0cb4a2d 100644
--- a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.2.eb
+++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb
@@ -1,7 +1,7 @@
 easyblock = 'Binary'
 
 name = 'Nextflow'
-version = '24.04.2'
+version = '24.10.2'
 
 homepage = 'https://www.nextflow.io/'
 description = """Nextflow is a reactive workflow framework and a programming DSL
@@ -10,26 +10,27 @@ description = """Nextflow is a reactive workflow framework and a programming DSL
 toolchain = SYSTEM
 
 source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/']
-sources = ['nextflow-%(version)s-all']
-checksums = ['1491a4efc06f0df9eed1fa6aa5a8c657435397fa99c34bf954281460e9b1c5ee']
+sources = ['nextflow-%(version)s-dist']
+checksums = ['972bb4f4bcd30bb474c29c247ccf79289bbcd444f799f0307f61123e6b0f7475']
 
-dependencies = [('Java', '11')]
+dependencies = [('Java', '21')]
 
 install_cmds = [
     "mkdir -p %(installdir)s/bin",
-    "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin",
-    "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow",
-    "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-all",
+    "cp %(builddir)s/nextflow-%(version)s-dist %(installdir)s/bin",
+    "cd %(installdir)s/bin && ln -s nextflow-%(version)s-dist nextflow",
+    "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-dist",
 ]
 
 sanity_check_paths = {
-    'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'],
+    'files': ['bin/nextflow-%(version)s-dist', 'bin/nextflow'],
     'dirs': []
 }
 
 sanity_check_commands = [
     "nextflow -v",
     "nextflow help",
+    "nextflow info",
 ]
 
 moduleclass = 'tools'
Diff against Nextflow-23.10.0.eb

easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb

diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb
index 2c6f2b030c..75b0cb4a2d 100644
--- a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb
+++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb
@@ -1,7 +1,7 @@
 easyblock = 'Binary'
 
 name = 'Nextflow'
-version = '23.10.0'
+version = '24.10.2'
 
 homepage = 'https://www.nextflow.io/'
 description = """Nextflow is a reactive workflow framework and a programming DSL
@@ -10,26 +10,27 @@ description = """Nextflow is a reactive workflow framework and a programming DSL
 toolchain = SYSTEM
 
 source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/']
-sources = ['nextflow-%(version)s-all']
-checksums = ['c69f6055c97741b828b6ee67de38125a42f1774f1621afd34c0eb72ffea171a6']
+sources = ['nextflow-%(version)s-dist']
+checksums = ['972bb4f4bcd30bb474c29c247ccf79289bbcd444f799f0307f61123e6b0f7475']
 
-dependencies = [('Java', '11')]
+dependencies = [('Java', '21')]
 
 install_cmds = [
     "mkdir -p %(installdir)s/bin",
-    "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin",
-    "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow",
-    "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-all",
+    "cp %(builddir)s/nextflow-%(version)s-dist %(installdir)s/bin",
+    "cd %(installdir)s/bin && ln -s nextflow-%(version)s-dist nextflow",
+    "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-dist",
 ]
 
 sanity_check_paths = {
-    'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'],
+    'files': ['bin/nextflow-%(version)s-dist', 'bin/nextflow'],
     'dirs': []
 }
 
 sanity_check_commands = [
     "nextflow -v",
     "nextflow help",
+    "nextflow info",
 ]
 
 moduleclass = 'tools'

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@boegelbot please test @ generoso

@pavelToman pavelToman mentioned this pull request Nov 29, 2024
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@pavelToman: Request for testing this PR well received on login1

PR test command 'EB_PR=21939 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21939 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14784

Test results coming soon (I hope)...

- notification for comment with ID 2507840492 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/2fc6e5481f5d2f37d5b5da6589ddc8f8 for a full test report.

@pavelToman
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@boegelbot please test @ jsc-zen3

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@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21939 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21939 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5355

Test results coming soon (I hope)...

- notification for comment with ID 2507855706 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/427ccfc79074a04bbdd7951e01fd4415 for a full test report.

smoors
smoors approved these changes Nov 29, 2024
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lgtm

@smoors smoors added this to the release after 4.9.4 milestone Nov 29, 2024
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smoors commented Nov 29, 2024

Going in, thanks @pavelToman!

@smoors smoors merged commit 84b0ad6 into easybuilders:develop Nov 29, 2024
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Nextflow 24.10.0
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@pavelToman @boegelbot @smoors