add missing PEAR dependency in easyconfig for GBprocesS v2.3 + enhance sanity check

[zarybnicky]

(created using eb --new-pr)

[zarybnicky]

No idea how that sanity check could've worked but it does now. I've also discovered that a literal [General] inside a string somehow gets transformed into # Main block General causing me to take an unplanned deep dive into easybuild-framework...

[zarybnicky]

@boegel The recommended EOF seems to break unit tests "Failed to parse easyconfig, unexpected EOF", trying out EOS again.

[zarybnicky]

Alright, so it isn't the EOF/EOS, but the [General], I think. although I'm not sure how best to solve this - it works now that the [General] is not at the start of the line but at the end, it's just the unit tests that fail... Maybe there are two different parser implementations? I'm not sure, I didn't look inside the code yet, maybe tomorrow. @boegel

[boegel]

I was able to reproduce the issue outside of the tests, it's a problem with the dumped easyconfig file in which the value of local_gbprocess_cfg got interpolated into sanity_check_commands, leading to:

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 <<EOS
[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/

EOS""",
    "%(namelower)s --debug -c %(builddir)s/config.ini",
]

This leads to the eventual parsing error:

>>> EasyConfigParser('test.eb')
Traceback (most recent call last):
  File "/Users/kehoste/work/easybuild-framework/easybuild/framework/easyconfig/format/pyheaderconfigobj.py", line 196, in parse_pyheader
    exec(pyheader, cfg)
  File "<string>", line 41
    """cat > %(builddir)s/config.ini <<EOS
                                          ^
SyntaxError: EOF while scanning triple-quoted string literal

I danced around the issue in 0bc6d3a by creating the config.ini via echo commands in sanity_check_commands (which is ugly, but it works).

[boegel]

@boegelbot please test @ generoso

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3501.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/78a0e409813f1ce038d5c30a21c4379d for a full test report.

[boegelbot]

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11767 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11767 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 12240

Test results coming soon (I hope)...

- notification for comment with ID 739926287 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).

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3145.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/df8fec2fb0e2c7855cbb7c84a5407ec2 for a full test report.

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node2728.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/d58413ad0ccf00ce9250ec347ad1d898 for a full test report.

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/a3360333b1c2d469efc220a01774732e for a full test report.

[boegel]

Going in, thanks @zarybnicky!