{bio}[GCCcore/6.3.0] structure v2.3.4 #5202
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@cmeesters Thanks for your contribution. Please take a look at fixing these style issues: |
boegel
requested changes
Oct 10, 2017
| # HPC-group University of Mainz (https://hpc.uni-mainz.de) | ||
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| easyblock = 'MakeCp' | ||
| name = 'structure' |
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please include an empty line above, to match the style of existing easyconfigs
| homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html' | ||
| description = """The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include infering the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.""" | ||
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| toolchain = {'name': 'dummy', 'version': 'dummy'} |
There was a problem hiding this comment.
Any reason to use dummy rather than a 'proper' toolchain?
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| sanity_check_paths = {'files' : ['structure'], | ||
| 'dirs' : []} | ||
| #buildininstalldir = True |
There was a problem hiding this comment.
please remove commented out lines
| files_to_copy = ['structure'] | ||
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| sanity_check_paths = {'files' : ['structure'], | ||
| 'dirs' : []} |
There was a problem hiding this comment.
please reformat to:
sanity_check_paths = {
'files' : ['structure'],
'dirs' : [],
}|
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| source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/'] | ||
| sources = ['structure_kernel_source.tar.gz'] | ||
| files_to_copy = ['structure'] |
| toolchain = {'name': 'dummy', 'version': 'dummy'} | ||
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| source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/'] | ||
| sources = ['structure_kernel_source.tar.gz'] |
There was a problem hiding this comment.
If no properly versioned source tarball is available, please let EasyBuild rename it on download, and also include a SHA256 checksum:
sources = [{'download_filename': 'structure_kernel_source.tar.gz', 'filename': SOURCE_TAR_GZ}]
checksums = ['...']| 'dirs' : []} | ||
| #buildininstalldir = True | ||
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| #installopts = 'PREFIX=%(installdir)s' |
There was a problem hiding this comment.
please remove commented out lines
| #buildininstalldir = True | ||
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| #installopts = 'PREFIX=%(installdir)s' | ||
| moduleclass = 'bio' |
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| allow_prepend_abs_path = True | ||
| modextrapaths = {'PATH': '%(installdir)s' } |
There was a problem hiding this comment.
you don't need allow_prepend_abs_path = True here, just use:
modextrapaths = {'PATH': ''}(the installation prefix is prepended automatically for all entries)
Also, please move this up, above the moduleclass = ... line
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Dear Kenneth,
Thank you for your detailed comments. I will certainly clean this up
(tomorrow).
Best regards,
Christian
…On 10/10/2017 08:36 PM, Kenneth Hoste wrote:
***@***.**** requested changes on this pull request.
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> @@ -0,0 +1,27 @@
+# This file is an EasyBuild recipy by Christian Meesters (2017)
+# HPC-group University of Mainz (https://hpc.uni-mainz.de)
+
+easyblock = 'MakeCp'
+name = 'structure'
please include an empty line above, to match the style of existing
easyconfigs
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> @@ -0,0 +1,27 @@
+# This file is an EasyBuild recipy by Christian Meesters (2017)
+# HPC-group University of Mainz (https://hpc.uni-mainz.de)
+
+easyblock = 'MakeCp'
+name = 'structure'
+version = '2.3.4'
+
+homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html'
+description = """The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include infering the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
Any reason to use |dummy| rather than a 'proper' toolchain?
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> +easyblock = 'MakeCp'
+name = 'structure'
+version = '2.3.4'
+
+homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html'
+description = """The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include infering the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/']
+sources = ['structure_kernel_source.tar.gz']
+files_to_copy = ['structure']
+
+sanity_check_paths = {'files' : ['structure'],
+ 'dirs' : []}
+#buildininstalldir = True
please remove commented out lines
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> +
+easyblock = 'MakeCp'
+name = 'structure'
+version = '2.3.4'
+
+homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html'
+description = """The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include infering the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/']
+sources = ['structure_kernel_source.tar.gz']
+files_to_copy = ['structure']
+
+sanity_check_paths = {'files' : ['structure'],
+ 'dirs' : []}
please reformat to:
sanity_check_paths= {
'files' : ['structure'],
'dirs' : [],
}
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> @@ -0,0 +1,27 @@
+# This file is an EasyBuild recipy by Christian Meesters (2017)
+# HPC-group University of Mainz (https://hpc.uni-mainz.de)
+
+easyblock = 'MakeCp'
+name = 'structure'
+version = '2.3.4'
+
+homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html'
+description = """The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include infering the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/']
+sources = ['structure_kernel_source.tar.gz']
+files_to_copy = ['structure']
empty line above please
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> @@ -0,0 +1,27 @@
+# This file is an EasyBuild recipy by Christian Meesters (2017)
+# HPC-group University of Mainz (https://hpc.uni-mainz.de)
+
+easyblock = 'MakeCp'
+name = 'structure'
+version = '2.3.4'
+
+homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html'
+description = """The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include infering the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/']
+sources = ['structure_kernel_source.tar.gz']
If no properly versioned source tarball is available, please let
EasyBuild rename it on download, and also include a SHA256 checksum:
sources= [{'download_filename':'structure_kernel_source.tar.gz','filename':SOURCE_TAR_GZ}]
checksums= ['...']
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> +version = '2.3.4'
+
+homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html'
+description = """The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include infering the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/']
+sources = ['structure_kernel_source.tar.gz']
+files_to_copy = ['structure']
+
+sanity_check_paths = {'files' : ['structure'],
+ 'dirs' : []}
+#buildininstalldir = True
+
+#installopts = 'PREFIX=%(installdir)s'
please remove commented out lines
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> +
+homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html'
+description = """The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include infering the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/']
+sources = ['structure_kernel_source.tar.gz']
+files_to_copy = ['structure']
+
+sanity_check_paths = {'files' : ['structure'],
+ 'dirs' : []}
+#buildininstalldir = True
+
+#installopts = 'PREFIX=%(installdir)s'
+moduleclass = 'bio'
this should be the last line
------------------------------------------------------------------------
In easybuild/easyconfigs/s/structure/structure-2.3.4.eb
<#5202 (comment)>:
> +
+source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/']
+sources = ['structure_kernel_source.tar.gz']
+files_to_copy = ['structure']
+
+sanity_check_paths = {'files' : ['structure'],
+ 'dirs' : []}
+#buildininstalldir = True
+
+#installopts = 'PREFIX=%(installdir)s'
+moduleclass = 'bio'
+
+
+
+allow_prepend_abs_path = True
+modextrapaths = {'PATH': '%(installdir)s' }
you don't need |allow_prepend_abs_path = True| here, just use:
modextrapaths= {'PATH':''}
(the installation prefix is prepended automatically for all entries)
Also, please move this up, above the |moduleclass = ...| line
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#5202 (review)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AJaOS_rfeE2Y26CK1zldhl3lKHryg5xfks5sq7kRgaJpZM4P0MRw>.
--
Dr. Christian Meesters
Johannes Gutenberg-Universität Mainz
Zentrum für Datenverarbeitung
Anselm-Franz-von-Bentzelweg 12
55099 Mainz
tel. +49 (0)6131 39 26397
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boegel
requested changes
Oct 11, 2017
| It can be applied to most of the commonly-used genetic markers, including SNPS, | ||
| microsatellites, RFLPs and AFLPs.""" | ||
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| toolchain = {'name': 'GCC', 'version': '6.3.0'} |
There was a problem hiding this comment.
This toolchain doesn't exist, you should either use GCCcore/6.3.0 or GCC/6.3.0-2.28 (I strongly recommend the latter, since that toolchain already includes binutils, otherwise you need to list binutils yourself as a build dependency)
boegel
requested changes
Oct 11, 2017
| It can be applied to most of the commonly-used genetic markers, including SNPS, | ||
| microsatellites, RFLPs and AFLPs.""" | ||
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| toolchain = {'name': 'GCCcore', 'version': '6.3.0'} |
There was a problem hiding this comment.
@cmeesters As I mentioned, if you use GCCcore as toolchain, you need to include binutils as a build dependency.
Also, please remove the other easyconfigs, should work with eb --update-pr 5202 :structure-2.3.4.eb
boegel
requested changes
Oct 12, 2017
| # use same binutils version that was used when building GCC toolchain | ||
| builddependencies = [ | ||
| ('binutils', '2.27', '', True) | ||
| ] |
There was a problem hiding this comment.
@cmeesters This should go in the other easyconfig file, where you use GCCcore as toolchain. And this easyconfig file, that uses GCC should be removed.
Or, you should remove the easyconfig file using GCCcore as toolchain, and keep the one that uses GCC but then remove binutils as a build dep there...
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Build failure for me on |
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Sorry for the long lag and happy new year for everyone reading along. I tried this under SL6 (which should fairly well resemble a Centos6-setting) and did not get it work, as the glibc is outdated. D'oh! What is to conclude? Either it ought to work on every system - in this case I should withdraw this pull request. Or is works sufficiently well on recent systems. I will not invest more time in this config (rather in others), but would appreciate a brief comment. Best, |
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@cmeesters The problems are probably caused because of a missing build dependency on When using We now have a check for this, see #5436, but this was not in place yet when you opened this pull request. I'll close and re-open this PR to make Travis re-test it, which should make the tests fail. If you fix that issue, the build should work everywhere, indeed. Another way to fix this would be to only retain |
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@ccmeesters ping? this seems to be almost ready, only missing either of @boegel's suggestions above |
boegel
changed the title
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@cmeesters, this PR is being closed for the following reason(s): no activity for > 6 months. |
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(created using
eb --new-pr)