{bio}[gompi/2023a] Kraken2 v2.1.3 #21834

PetrKralCZ · 2024-11-12T10:38:47Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#434

github-actions · 2024-11-12T10:43:09Z

Updated software `Kraken2-2.1.3-gompi-2023a.eb`

Diff against Kraken2-2.1.2-gompi-2022a.eb

easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb
index 9ed7324537..f4733d380e 100644
--- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb
+++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PackedBinary'
 
 name = 'Kraken2'
-version = '2.1.2'
+version = '2.1.3'
 
 homepage = 'https://github.com/DerrickWood/kraken2/wiki'
 description = """Kraken is a system for assigning taxonomic labels to short DNA sequences,
@@ -13,27 +13,25 @@ description = """Kraken is a system for assigning taxonomic labels to short DNA
  utilizing exact alignments of k-mers and a novel classification algorithm."""
 
 # part is compiled with $CXX, the rest is in Perl
-toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 toolchainopts = {'openmp': True, 'cstd': 'c++11'}
 
 github_account = 'DerrickWood'
 source_urls = [GITHUB_LOWER_SOURCE]
 sources = ['v%(version)s.tar.gz']
 patches = [
-    '%(name)s-2.1.1_fix_installation_for_easybuild.patch',
-    '%(name)s-%(version)s_fix_ncbi_https_server.patch',
+    '%(name)s-2.1.3_fix_installation_for_easybuild.patch',
 ]
 checksums = [
-    'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3',  # v2.1.2.tar.gz
-    # Kraken2-2.1.1_fix_installation_for_easybuild.patch
-    '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11',
-    '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116',  # Kraken2-2.1.2_fix_ncbi_https_server.patch
+    {'v2.1.3.tar.gz': '5269fa14adfb02e38c2da2e605e909a432d76c680d73e2e0e80e27ccd04d7c69'},
+    {'Kraken2-2.1.3_fix_installation_for_easybuild.patch':
+     'd2faecff258133033cb81d5ac70d1a7ff1b4323091411aa835a13de83f2cc174'},
 ]
 
 dependencies = [
-    ('Perl', '5.34.1'),
-    ('BLAST+', '2.13.0'),
-    ('wget', '1.21.3'),
+    ('Perl', '5.36.1'),
+    ('BLAST+', '2.14.1'),
+    ('wget', '1.24.5'),
 ]
 
 install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && '

Diff against Kraken2-2.1.2-gompi-2021b.eb

easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021b.eb

diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021b.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb
index 7e70470c5f..f4733d380e 100644
--- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021b.eb
+++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PackedBinary'
 
 name = 'Kraken2'
-version = '2.1.2'
+version = '2.1.3'
 
 homepage = 'https://github.com/DerrickWood/kraken2/wiki'
 description = """Kraken is a system for assigning taxonomic labels to short DNA sequences,
@@ -13,27 +13,25 @@ description = """Kraken is a system for assigning taxonomic labels to short DNA
  utilizing exact alignments of k-mers and a novel classification algorithm."""
 
 # part is compiled with $CXX, the rest is in Perl
-toolchain = {'name': 'gompi', 'version': '2021b'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 toolchainopts = {'openmp': True, 'cstd': 'c++11'}
 
 github_account = 'DerrickWood'
 source_urls = [GITHUB_LOWER_SOURCE]
 sources = ['v%(version)s.tar.gz']
 patches = [
-    '%(name)s-2.1.1_fix_installation_for_easybuild.patch',
-    '%(name)s-%(version)s_fix_ncbi_https_server.patch',
+    '%(name)s-2.1.3_fix_installation_for_easybuild.patch',
 ]
 checksums = [
-    'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3',  # v2.1.2.tar.gz
-    # Kraken2-2.1.1_fix_installation_for_easybuild.patch
-    '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11',
-    '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116',  # Kraken2-2.1.2_fix_ncbi_https_server.patch
+    {'v2.1.3.tar.gz': '5269fa14adfb02e38c2da2e605e909a432d76c680d73e2e0e80e27ccd04d7c69'},
+    {'Kraken2-2.1.3_fix_installation_for_easybuild.patch':
+     'd2faecff258133033cb81d5ac70d1a7ff1b4323091411aa835a13de83f2cc174'},
 ]
 
 dependencies = [
-    ('Perl', '5.34.0'),
-    ('BLAST+', '2.12.0'),
-    ('wget', '1.21.2'),
+    ('Perl', '5.36.1'),
+    ('BLAST+', '2.14.1'),
+    ('wget', '1.24.5'),
 ]
 
 install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && '
@@ -59,4 +57,12 @@ sanity_check_paths = {
     'dirs': [],
 }
 
+sanity_check_commands = [
+    'kraken2 --help',
+    'kraken2-build --help',
+    'kraken2-inspect --help',
+    'build_db -h',
+    'classify -h',
+]
+
 moduleclass = 'bio'

Diff against Kraken2-2.1.2-gompi-2021a.eb

easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb

diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb
index 9c1671e01b..f4733d380e 100644
--- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb
+++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PackedBinary'
 
 name = 'Kraken2'
-version = '2.1.2'
+version = '2.1.3'
 
 homepage = 'https://github.com/DerrickWood/kraken2/wiki'
 description = """Kraken is a system for assigning taxonomic labels to short DNA sequences,
@@ -13,27 +13,25 @@ description = """Kraken is a system for assigning taxonomic labels to short DNA
  utilizing exact alignments of k-mers and a novel classification algorithm."""
 
 # part is compiled with $CXX, the rest is in Perl
-toolchain = {'name': 'gompi', 'version': '2021a'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 toolchainopts = {'openmp': True, 'cstd': 'c++11'}
 
 github_account = 'DerrickWood'
 source_urls = [GITHUB_LOWER_SOURCE]
 sources = ['v%(version)s.tar.gz']
 patches = [
-    'Kraken2-2.1.1_fix_installation_for_easybuild.patch',
-    'Kraken2-2.1.2_fix_ncbi_https_server.patch',
+    '%(name)s-2.1.3_fix_installation_for_easybuild.patch',
 ]
 checksums = [
-    'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3',  # v2.1.2.tar.gz
-    # Kraken2-2.1.1_fix_installation_for_easybuild.patch
-    '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11',
-    '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116',  # Kraken2-2.1.2_fix_ncbi_https_server.patch
+    {'v2.1.3.tar.gz': '5269fa14adfb02e38c2da2e605e909a432d76c680d73e2e0e80e27ccd04d7c69'},
+    {'Kraken2-2.1.3_fix_installation_for_easybuild.patch':
+     'd2faecff258133033cb81d5ac70d1a7ff1b4323091411aa835a13de83f2cc174'},
 ]
 
 dependencies = [
-    ('Perl', '5.32.1'),
-    ('BLAST+', '2.11.0'),
-    ('wget', '1.21.1'),
+    ('Perl', '5.36.1'),
+    ('BLAST+', '2.14.1'),
+    ('wget', '1.24.5'),
 ]
 
 install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && '
@@ -59,4 +57,12 @@ sanity_check_paths = {
     'dirs': [],
 }
 
+sanity_check_commands = [
+    'kraken2 --help',
+    'kraken2-build --help',
+    'kraken2-inspect --help',
+    'build_db -h',
+    'classify -h',
+]
+
 moduleclass = 'bio'

PetrKralCZ · 2024-11-12T11:51:16Z

@boegelbot please test @ generoso

boegelbot · 2024-11-12T11:55:09Z

@PetrKralCZ: Request for testing this PR well received on login1

PR test command 'EB_PR=21834 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21834 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14691

Test results coming soon (I hope)...

- notification for comment with ID 2470329835 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).

boegelbot · 2024-11-12T11:55:35Z

Test report by @boegelbot
FAILED
Build succeeded for 0 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/95ebe88be89d6972427395db94681414 for a full test report.

PetrKralCZ · 2024-11-12T13:24:18Z

@boegelbot please test @ generoso

boegelbot · 2024-11-12T13:25:09Z

@PetrKralCZ: Request for testing this PR well received on login1

PR test command 'EB_PR=21834 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21834 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14692

Test results coming soon (I hope)...

- notification for comment with ID 2470522778 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).

boegelbot · 2024-11-12T13:26:43Z

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/65a5d4522693ddd57676a7d6a1c854a8 for a full test report.

PetrKralCZ · 2024-11-12T13:27:29Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-12T13:30:09Z

@PetrKralCZ: 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=21834 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21834 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5252

Test results coming soon (I hope)...

- notification for comment with ID 2470529553 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).

boegelbot · 2024-11-12T13:31:57Z

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 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/26447cf612fa0e89e5196c5b8ee2c314 for a full test report.

verdurin · 2024-12-10T15:13:44Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/e458e13a32a41e60d44644631ab868ba for a full test report.

verdurin

Looks fine.

verdurin · 2024-12-10T15:17:58Z

Going in, thanks @PetrKralCZ!

adding easyconfigs: Kraken2-2.1.3-gompi-2023a.eb

bb1d9ab

PetrKralCZ added the update label Nov 12, 2024

PetrKralCZ mentioned this pull request Nov 12, 2024

Kraken2 vscentrum/vsc-software-stack#434

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add patch file

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verdurin added this to the release after 4.9.4 milestone Dec 10, 2024

verdurin approved these changes Dec 10, 2024

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verdurin merged commit 4acc7df into easybuilders:develop Dec 10, 2024
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{bio}[gompi/2023a] Kraken2 v2.1.3 #21834

{bio}[gompi/2023a] Kraken2 v2.1.3 #21834

PetrKralCZ commented Nov 12, 2024 •

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{bio}[gompi/2023a] Kraken2 v2.1.3 #21834

{bio}[gompi/2023a] Kraken2 v2.1.3 #21834

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Updated software Kraken2-2.1.3-gompi-2023a.eb

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PetrKralCZ commented Nov 12, 2024 •

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Updated software `Kraken2-2.1.3-gompi-2023a.eb`