Philosopher 3.2.9

[fizwit]

(created using eb --new-pr)

[migueldiascosta]

@fizwit I have no experience with Go but could the new (since eb 4.2.1) GoPackage easyblock (easybuilders/easybuild-easyblocks#2042) be used here, instead of the binary tarball?

cc @Darkless012

[Darkless012]

Yup, GoPackage is way to go. Unfortunately I wasn't able to build the package. I'm including easyconfig used and error message.

easyblock = 'GoPackage'

name = 'philosopher'
version = '3.2.9'

homepage = 'https://github.com/Nesvilab/philosopher/wiki'
description = """Philosopher provides easy access to third-party tools and custom algorithms
 allowing users to develop proteomics analysis, from Peptide Spectrum Matching to annotated
 protein reports. Philosopher is also tuned for Open Search analysis, providing a modified
 version of the prophets for peptide validation and protein inference. To this date, Philosopher
 is the only proteomics toolkit that allows you to process and analyze close and
 open search results."""

toolchain = SYSTEM

# https://github.com/Nesvilab/philosopher
github_account = 'Nesvilab'
source_urls = [GITHUB_SOURCE]
sources = ['v%(version)s.tar.gz']
checksums = ['767cba171ed2792952603e20570a1fec367b3311d61e025b8a1c00e79ef6f9a0']

builddependencies = [
    ('Go', '1.14.1'),
]
dependencies = [('Java', '1.8')]

moduleclass = 'bio'

ERROR:

== FAILED: Installation ended unsuccessfully (build directory: /tmp/vsc43143/easybuild/build/philosopher/3.2.9/system-system): build failed (first 300 chars): cmd " go install " exited with exit code 2 and output:
# philosopher/lib/ext/cdhit/unix
lib/ext/cdhit/unix/unix.go:15:13: undefined: Asset
# philosopher/lib/ext/peptideprophet/unix
lib/ext/peptideprophet/unix/unix.go:14:13: undefined: Asset
...

[Darkless012]

Tarball can be easier option, but it is compiled binary with all its pros and cons.

[Darkless012]

Apparently it has its own build procedure:
https://github.com/Nesvilab/philosopher/blob/8f389e2fd53dafde5fdcb16d7c5703e0b8f7326a/.github/workflows/go.yml

...with copying stuff here and there 👎 ...

[Micket]

Just a comment, either approach we go for, should have a -Java-%(javaver)s versionsuffix. If we start having gopackages outside toolchains as well, then the same applies there, we should probably need a -Go-XXX suffix as well.

[Darkless012]

Gopackage is outside of toolchain (SYSTEM), but Go is needed only on build time. Then it should be just executable.
Having -Go-XXX suffix, would sign, two different go versions can't be combined, but this is not true, since only binaries are left?

[fizwit]

Instructions for building from philosopher from source were just published. I am resubmitting the EasyConfig.

[fizwit]

Philosopher does not need a --Go-XX suffix. Go is only a build dependency that creates a binary.

[Micket]

Does Go not have any standard library that it links to?

[Darkless012]

AFAIK it doesn't. Go produces self-contained executable.

[fizwit]

Philosopher 4 has changed significantly. I will work on a newer easyconfig for v4.