Cufflinks, TopHat easyconfig contributions

[claczny]

enjoy, 2 blocks are coming your way, too.

Signed-off-by: Cedric Laczny cedric.laczny@uni.lu

[JensTimmerman]

Looking good, but could you check your indentations? (tabs vs spaces??)

[claczny]

Ok, this is a recurring theme for me… Sorry.

What would be your preferences? Do you have maybe a vim modeling for me?

Thank you.

Best,

Cedric

On 7 Dec 2012, at 16:01, Jens Timmerman wrote:

Looking good, but could you check your indentations? (tabs vs spaces??)

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Cedric Laczny,
PhD Student

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | House of Biomedicine
7, avenue des Hauts-Fourneaux
L-4362 Esch-sur-Alzette
T +352 46 66 44 6398
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cedric.laczny@uni.lu http://lcsb.uni.lu

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[JensTimmerman]

this is in my .vimrc:

:set tabstop=4
:set shiftwidth=4
:set expandtab

[fgeorgatos]

re-review!

[JensTimmerman]

Are the attached patches really needed?

++    BAM_LIB="${EBROOTSAMTOOLS}/lib/libbam.a"

I suspect this should be found if Samtools set's it's library path correctly?
Or is there something else going on?

[JensTimmerman]

Looking good otherwise

[boegel]

I agree with @JensTimmerman, it this really needed? I don't see why it would fail.

Maybe because there's no .so provided by SamTools? If so, then that should be fixed instead, I think.

Same remark for the TopHat patch.

[claczny]

Actually, I think that was the case. If this was the case, I don't know how this could/should be changed. Cufflinks also has an --with-bam-libdir option for configure, so hopefully the "-lbam" would be correctly expanded.

[boegel]

Can you try and use the --with-bam-libdir option, without using this patch?

Just set configopts = '--with-bam-libdir=${EBROOTBAM}lib' in your easyconifg, and remove the patches line.

Let us know if that works, and if not, how it fails.

I'd prefer avoiding a patch if it's not really required (since that's an extra dependency for the build to work, next to the easyblock and the easyconfig file).

[fgeorgatos]

Hi there,

we just dropped oases from the pack so that it doesn't hold the rest; we'll see what to do with it a bit later.
(ditto for easyblocks... kindly check)

[JensTimmerman]

Indentation is off again

[JensTimmerman]

Except for the indentation this looks good to me.

[fgeorgatos]

Hi guys,

I fixed it, I don't know how it managed to creep in...

In the meantime, I also noticed the following (not fixed yet, TBD):

claczny@gaia-61:~/easybuild-easyconfigs/easybuild/easyconfigs/c/Cufflinks $ grep -P '\t' ../../*/*/*eb
../../c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb:           ('SAMtools', '0.1.18'),
../../c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb:           ('Eigen', '3.1.1')
../../g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb:                   }
../../g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb:       ('libtool', '2.4.2'),
../../g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb:       ('GMP', '5.0.5'),
../../g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb:       ('libunistring', '0.9.3'),
../../g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb:       ('pkg-config', '0.27.1'),
../../g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb:       ('libffi', '3.0.11'),
../../g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb:       ]
../../g/guile/guile-1.8.8-ictce-4.0.6.eb:       ('libtool', '2.4.2'),
../../g/guile/guile-1.8.8-ictce-4.0.6.eb:       ('GMP', '5.0.5'),
../../g/guile/guile-1.8.8-ictce-4.0.6.eb:       ('libunistring', '0.9.3'),
../../g/guile/guile-1.8.8-ictce-4.0.6.eb:       ('pkg-config', '0.27.1'),
../../g/guile/guile-1.8.8-ictce-4.0.6.eb:       ('libffi', '3.0.11'),
../../g/guile/guile-1.8.8-ictce-4.0.6.eb:       ]
../../h/HDF5/HDF5-1.8.7-goalf-1.1.0-no-OFED-parallel.eb:        ('zlib', '1.2.7'),
../../h/HDF5/HDF5-1.8.7-goalf-1.1.0-no-OFED-parallel.eb:        ('Szip', '2.1'),
../../h/HDF5/HDF5-1.8.7-goalf-1.1.0-no-OFED-parallel.eb:        ]
../../l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb:       ('flex', '2.5.35'),
../../l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb:       ('Bison', '2.5'),
../../l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb:       ('byacc', '20120526'),
../../l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb:       ('guile', '1.8.8'),
../../l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb:       ]
../../l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb:       ('flex', '2.5.35'),
../../l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb:       ('Bison', '2.5'),
../../l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb:       ('byacc', '20120526'),
../../l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb:       ('guile', '1.8.8'),
../../l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb:       ]
../../l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb:      ('zlib', '1.2.7'),
../../l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb:      ('Python', pythonver),
../../l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb:      ]
../../l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb:      ('zlib', '1.2.7'),
../../l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb:      ('Python', pythonver),
../../l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb:      ]

[boegel]

remove the patches line, with the configopts set like they are, it should work

Also, get rid of the patch files (both of them), if we don't use them, they shouldn't be there.

You can always find them back via commit history is you really need to.

If you clean that up, it should be good to merge in.

[boegel]

Can you guys open separate pull requests for the Oases easyblock and easyconfig? I don't want that effort to go to waste. Just throw in there whatever you have now, and I'll help out to get it working and ready for merging in. Not doing it now will result in letting it rot away in some branch, which would be a shame.

[boegel]

After including claczny/easybuild-easyblocks#1 into easyblocks and claczny#1 into easyconfigs, this is ready to merge.

Tested both the Tophat and Cufflinks builds on my end, works great.

[boegel]

Merge should be fixed by claczny#2

[boegel]

Oases pull requests in easybuilders/easybuild-easyblocks#79 and #85.

[JensTimmerman]

arent' there any working intel compiler versions of cufflinks easyconfigs / patches?

[boegel]

@JensTimmerman: see #594