{bio}[system/system] picard v3.3.0 w/ Java 17

[PhoenixEmik]

(created using eb --new-pr)

[github-actions]

Updated software picard-3.3.0-Java-17.eb

Diff against picard-3.0.0-Java-17.eb

easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb

diff --git a/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb
index b9cd29fae7..8aafd64519 100644
--- a/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb
+++ b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb
@@ -24,12 +24,14 @@
 # Christoph Siegert (Leipzig University)
 # 3.0.0
 # Graham Derryberry (UTK)
+# 3.3.0
+# Emik Lin (HKUMed CPOS)
 ##
 
 easyblock = 'JAR'
 
 name = 'picard'
-version = '3.0.0'
+version = '3.3.0'
 versionsuffix = '-Java-%(javaver)s'
 
 homepage = 'https://broadinstitute.github.io/picard/'
@@ -42,7 +44,7 @@ sources = [{
     'filename': '%(name)s-%(version)s.jar',
     'download_filename': '%(name)s.jar',
 }]
-checksums = ['0d5e28ab301fad3b02030d01923888129ba82c5f722ac5ccb2d418ab76ac5499']
+checksums = ['58819a7660646b74b34e282f5d4d21c8dbaea22ddeff96e3258755dafa0f86dc']
 
 postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"]
 

Diff against picard-2.26.10-Java-15.eb

easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb

diff --git a/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb
index 342591127c..8aafd64519 100644
--- a/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb
+++ b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb
@@ -22,12 +22,16 @@
 # Erica Bianco (HPCNow!)
 # 2.26.10
 # Christoph Siegert (Leipzig University)
+# 3.0.0
+# Graham Derryberry (UTK)
+# 3.3.0
+# Emik Lin (HKUMed CPOS)
 ##
 
 easyblock = 'JAR'
 
 name = 'picard'
-version = '2.26.10'
+version = '3.3.0'
 versionsuffix = '-Java-%(javaver)s'
 
 homepage = 'https://broadinstitute.github.io/picard/'
@@ -40,11 +44,11 @@ sources = [{
     'filename': '%(name)s-%(version)s.jar',
     'download_filename': '%(name)s.jar',
 }]
-checksums = ['84a056466cf23155e2126b33fde61b5485217b365d4899c1bdc82fe9284f2395']
+checksums = ['58819a7660646b74b34e282f5d4d21c8dbaea22ddeff96e3258755dafa0f86dc']
 
 postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"]
 
-dependencies = [('Java', '15')]
+dependencies = [('Java', '17')]
 
 sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE']
 

Diff against picard-2.25.5-Java-13.eb

easybuild/easyconfigs/p/picard/picard-2.25.5-Java-13.eb

diff --git a/easybuild/easyconfigs/p/picard/picard-2.25.5-Java-13.eb b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb
index dde956fdf6..8aafd64519 100644
--- a/easybuild/easyconfigs/p/picard/picard-2.25.5-Java-13.eb
+++ b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb
@@ -20,12 +20,18 @@
 # J. Sassmannshausen (GSTT)
 # 2.25.5
 # Erica Bianco (HPCNow!)
+# 2.26.10
+# Christoph Siegert (Leipzig University)
+# 3.0.0
+# Graham Derryberry (UTK)
+# 3.3.0
+# Emik Lin (HKUMed CPOS)
 ##
 
 easyblock = 'JAR'
 
 name = 'picard'
-version = '2.25.5'
+version = '3.3.0'
 versionsuffix = '-Java-%(javaver)s'
 
 homepage = 'https://broadinstitute.github.io/picard/'
@@ -38,11 +44,13 @@ sources = [{
     'filename': '%(name)s-%(version)s.jar',
     'download_filename': '%(name)s.jar',
 }]
-checksums = ['f7fa9784b84d384abfcbd77076f5ceab7b2797dc863ac35fd41470daa3efe3a5']
+checksums = ['58819a7660646b74b34e282f5d4d21c8dbaea22ddeff96e3258755dafa0f86dc']
 
 postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"]
 
-dependencies = [('Java', '13')]
+dependencies = [('Java', '17')]
+
+sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE']
 
 sanity_check_paths = {
     'files': ['picard.jar'],

[PhoenixEmik]

Test report by @PhoenixEmik
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
rocky-8-build - Linux Rocky Linux 8.10, x86_64, AMD Ryzen 7 7840HS w/ Radeon 780M Graphics, Python 3.6.8
See https://gist.github.com/PhoenixEmik/a0b9a962a7991df9dd0d1f9a1c8f5f59 for a full test report.

[verdurin]

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/1bfd937f98b2ebeb68a827fc9b8fe5b7 for a full test report.

[verdurin]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=21913 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21913 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 14773

Test results coming soon (I hope)...

- notification for comment with ID 2505738876 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]

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/b6feb00f04d9cdd32c833d03e529b29c for a full test report.

[verdurin]

@boegelbot please test @ jsc-zen3

[boegelbot]

@verdurin: 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=21913 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21913 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5345

Test results coming soon (I hope)...

- notification for comment with ID 2505754580 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]

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/9074c0a0ab1c643c3a9d7baa080f2906 for a full test report.

[verdurin]

Looks fine.

[verdurin]

@PhoenixEmik thanks for your contribution, and welcome to EasyBuild.

[verdurin]

Going in, thanks @PhoenixEmik!