From 8d34b6e34d4bb1ec33b6414ffac544010b2ec918 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 25 Nov 2020 23:33:21 +0100 Subject: [PATCH 1/5] {bio}[intel/2020a] GBprocesS v2.3, PEAR 0.9.11 --- .../GBprocesS-2.3-intel-2020a-Python-3.8.2.eb | 15 ++++++++ .../p/PEAR/PEAR-0.9.11-GCCcore-9.3.0.eb | 34 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb index db57ce63fd55..af447b077196 100644 --- a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb @@ -22,6 +22,7 @@ dependencies = [ ('Python', '3.8.2'), ('cutadapt', '2.10', '-Python-%(pyver)s'), ('Biopython', '1.78', versionsuffix), + ('PEAR', '0.9.11'), ] use_pip = True @@ -38,6 +39,20 @@ pretestopts = ( runtest = 'python -m unittest discover -v -s ./test -p test_*.py' +sanity_check_commands = [ + 'export TEMP=$(mktemp -d)' + ''' && echo > $TEMP/config.ini < Date: Thu, 26 Nov 2020 18:36:24 +0100 Subject: [PATCH 2/5] GBprocesS: reformat sanity check --- .../GBprocesS-2.3-intel-2020a-Python-3.8.2.eb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb index af447b077196..b21fac1b2c8f 100644 --- a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb @@ -39,18 +39,20 @@ pretestopts = ( runtest = 'python -m unittest discover -v -s ./test -p test_*.py' -sanity_check_commands = [ - 'export TEMP=$(mktemp -d)' - ''' && echo > $TEMP/config.ini < %(builddir)s/config.ini < Date: Thu, 26 Nov 2020 19:02:41 +0100 Subject: [PATCH 3/5] GBprocesS: fix sanity check --- .../GBprocesS-2.3-intel-2020a-Python-3.8.2.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb index b21fac1b2c8f..7c562ed9b23c 100644 --- a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb @@ -41,17 +41,18 @@ runtest = 'python -m unittest discover -v -s ./test -p test_*.py' # Trivial configuration file to use when running gbprocess sanity check # See https://gitlab.com/dschaumont/GBprocesS/-/blob/master/docs/user_guide.rst -local_gbprocess_cfg = """ -# Main block General +local_gbprocess_cfg = """[General] cores = 1 -input_directory = /data/run/ +input_directory = %(builddir)s/ sequencing_type = pe -input_file_name_template = {run:24}_R{orientation:1}_001{extension:10} +input_file_name_template = {run:25}_R{orientation:1}_001{extension} temp_dir = %(builddir)s/ """ sanity_check_commands = [ - "echo > %(builddir)s/config.ini < %(builddir)s/config.ini < Date: Thu, 26 Nov 2020 21:37:25 +0100 Subject: [PATCH 4/5] GBprocesS: EOF breaks unit tests, maybe EOS? --- .../g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb index 7c562ed9b23c..0b467f61f2f1 100644 --- a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb @@ -52,7 +52,7 @@ temp_dir = %(builddir)s/ sanity_check_commands = [ "touch %(builddir)s/17146FL-13-01-01_S97_L002_R1_001.fastq", "touch %(builddir)s/17146FL-13-01-01_S97_L002_R2_001.fastq", - "cat > %(builddir)s/config.ini < %(builddir)s/config.ini < Date: Mon, 7 Dec 2020 14:39:42 +0100 Subject: [PATCH 5/5] create config.ini to run sanity check command via echo commands in sanity_check_commands to dance around test failure with dumped easyconfig --- .../GBprocesS-2.3-intel-2020a-Python-3.8.2.eb | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb index 0b467f61f2f1..f0eb2e141fb8 100644 --- a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb @@ -39,20 +39,17 @@ pretestopts = ( runtest = 'python -m unittest discover -v -s ./test -p test_*.py' -# Trivial configuration file to use when running gbprocess sanity check -# See https://gitlab.com/dschaumont/GBprocesS/-/blob/master/docs/user_guide.rst -local_gbprocess_cfg = """[General] -cores = 1 -input_directory = %(builddir)s/ -sequencing_type = pe -input_file_name_template = {run:25}_R{orientation:1}_001{extension} -temp_dir = %(builddir)s/ -""" - sanity_check_commands = [ "touch %(builddir)s/17146FL-13-01-01_S97_L002_R1_001.fastq", "touch %(builddir)s/17146FL-13-01-01_S97_L002_R2_001.fastq", - "cat > %(builddir)s/config.ini < %(builddir)s/config.ini", + "echo 'cores = 1' >> %(builddir)s/config.ini", + "echo 'input_directory = %(builddir)s/' >> %(builddir)s/config.ini", + "echo 'sequencing_type = pe' >> %(builddir)s/config.ini", + "echo 'input_file_name_template = {run:25}_R{orientation:1}_001{extension}' >> %(builddir)s/config.ini", + "echo 'temp_dir = %(builddir)s/' >> %(builddir)s/config.ini", "gbprocess --debug -c %(builddir)s/config.ini", ]