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Chymera
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PostPosted: Fri Sep 27, 2013 1:05 am    Post subject: Neuroscience on Gentoo Reply with quote

Hi guys, I have recently started writing ebuilds for some very important software packages used in brain imaging analysis. The ones NOT in the gentoo-science overlay are as follows:

- SPM ( 8 ) https://github.com/gentoo-science/sci/pull/107
- FSL https://github.com/TheChymera/sci/blob/fsl/sci-biology/fsl/fsl-5.0.4.ebuild (no pull request yet)
- AFNI https://github.com/gentoo-science/sci/pull/115

I have been working on these ebuilds for around 3 weeks, and it really seems I've exhausted my ebuilding knowledge. I have learned a lot in this time, but I seem to notice how the amount of time I can invest in this isn't enough to get things working in the foreseeable future.

I'd like to ask any of you if you would think it worthwhile to have these software packages on Gentoo (I am sure there are other neuroscientists except me using this fabulous distribution, and if there aren't we should take care of attracting them) - and if you would be willing to lend a helping hand.

I'm not asking you to finish my work for me, I'll still do whatever I can do on a daily basis - it's just that me + occasionally 2 gentoo-science devs doesn't seem to get this done.

Many Thanks,
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christian.
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PostPosted: Fri Sep 27, 2013 2:29 pm    Post subject: Re: Neuroscience on Gentoo Reply with quote

Chymera wrote:
them) - and if you would be willing to lend a helping hand.

I'm not asking you to finish my work for me, I'll still do whatever I can do on a daily basis - it's just that me + occasionally 2 gentoo-science devs doesn't seem to get this done.

Hey there,

I just fiddled a bit with one of your ebuilds. It would probably help your case if you would give some more detailed information about the problems you are having. This way people might apply their knowledge more readily to your problem.

I am putting a patch for "sci-biology/spm" against your version at the end of this post. This patch installs fine on my system. I doubt I really solved any of your problems with those tiny changes. But, it solves this problem I had with your sci-biology/spm:

Code:
>>> Done src_unpack 
>>> Starting builtin_saveenv 
>>> Done builtin_saveenv 
>>> Completed ebuild phases loadenv unpack saveenv 
>>> Running ebuild phases loadenv prepare saveenv as paludisbuild:paludisbuild... 
>>> Starting builtin_loadenv 
>>> Done builtin_loadenv 
 
Error: 
  * In program cave perform install --hooks --managed-output --output-exclusivity with-others =sci-biology/spm-8:8::5till9 --destination installed --replacing =sci-biology/spm-8-r1:8::installed --x-of-y 1 of 1: 
  * When installing 'sci-biology/spm-8:8::5till9' replacing { 'sci-biology/spm-8-r1:8::installed' }: 
  * When running an ebuild command on 'sci-biology/spm-8:8::5till9': 
  * Install failed for 'sci-biology/spm-8:8::5till9' (paludis::ActionFailedError) 
 
 
!!! ERROR in sci-biology/spm-8::5till9: 
!!! In ebuild_f_prepare at line 39 
!!! ${S} ("/var/tmp/paludis/sci-biology-spm-8/work/spm") does not exist 
 
!!! Call stack: 
!!!    * ebuild_f_prepare (/usr/libexec/paludis/2/src_prepare.bash:39) 
!!!    * ebuild_main (/usr/libexec/paludis/ebuild.bash:673) 
!!!    * main (/usr/libexec/paludis/ebuild.bash:696) 
 
diefunc: making ebuild PID 129699 exit with error 
die trap: exiting with error. 
 
Failed install to / for sci-biology/spm-8:8::5till9 replacing 8-r1:8::installed 


What did I do:

  • changed $S -- fixing the problem above
  • reordered RDEPEND and DEPEND, because DEPEND was using RDEPEND
  • added a KEYWORD for "amd64" because I was to lazy to unmask it :) This should probably be reverted.
  • I didn't know why this would be a "live" ebuild, so I am using SRC_URI. I mean, according to the timestamp the last time the file at that URL was updated was over half a year ago


Code:
--- spm-8.ebuild        2013-09-27 15:08:03.211507799 +0100
+++ spm-8-r1.ebuild     2013-09-27 15:08:20.283563830 +0100
@@ -4,30 +4,21 @@
 
 EAPI=5
 
-inherit unpacker
-
 DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab"
 HOMEPAGE="http://www.fil.ion.ucl.ac.uk/spm/"
 URI_BASE="http://www.fil.ion.ucl.ac.uk/spm/download/restricted/idyll/"
-SRC_URI="" # SRC_URI is left blank on live ebuild
+SRC_URI="${URI_BASE}${PN}${PV}.zip"
 
 LICENSE="GPL-2+"
 SLOT="8"
-KEYWORDS=""
+KEYWORDS="amd64"
 
-DEPEND="${RDEPEND}
-       "
+S=${WORKDIR}/${PN}${PV}
 
 RDEPEND=">=sci-mathematics/octave-3.6.4
        "
-
-S=${WORKDIR}/${PN}
-
-src_unpack() {
-       # We have to do this inside of here, since it's a live ebuild. :-(
-       wget "${URI_BASE}${PN}${PV}.zip" || die
-       unpack "./${PN}${PV}.zip"
-       }
+DEPEND="${RDEPEND}
+       "
 
 src_prepare() {
        emake -C src distclean PLATFORM=octave
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Chymera
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PostPosted: Fri Sep 27, 2013 3:17 pm    Post subject: Reply with quote

Many thanks for your input. Are you by any chance on github? it would be great to have all conversations in one place (that being the pull request) since otherwise progress gets hard to keep track of.

S=${WORKDIR}/${PN}${PV}

Why did you replace that with

S=${WORKDIR}/${PN}

?

The package gets unpacked to .../spm8, not .../spm
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christian.
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PostPosted: Sun Sep 29, 2013 1:23 pm    Post subject: Reply with quote

Chymera wrote:
Many thanks for your input. Are you by any chance on github?
it would be great to have all conversations in one place (that being the pull
request) since otherwise progress gets hard to keep track of.

I could make a pull request on your repository with that patch. But it remains
to be seen if and how much more time I will put into this. I have no affiliation
with neuroscience nor am I using SPM. It was more like my good deed for the
day. But, let's see where it goes. :) I made a pull request for some the changes to spm-8 you did not consider from my patch. Comment away.

Chymera wrote:
S=${WORKDIR}/${PN}${PV}

Why did you replace that with

S=${WORKDIR}/${PN}

Actually, it was the other way around. :) I removed
Code:
-S=${WORKDIR}/${PN}

and added
Code:
+S=${WORKDIR}/${PN}${PV}

Maybe I accidentally grabbed an older version from your repository, since it is fine now on your side.
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Chymera
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PostPosted: Sun Sep 29, 2013 10:52 pm    Post subject: Reply with quote

Thanks for the pull request. And many thanks for your involvement - I would very much appreciate any other patches - as I said, especially on the FSL build which at present installs only one README file (out of the 1.3 GB of the source) o.0.

Have an awesome day!
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Chymera
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PostPosted: Thu Oct 03, 2013 6:16 am    Post subject: Reply with quote

In search for further generous and enthusiastic contributors I have described the state of the NeuroGentoo project in this public post.

I would be very grateful if - even if you yourself cannot contribute - you could disseminate this among neuro-enthusiastic or gentoo-enthusiastic contacts of yours. Apparently one maintainer is not enough :(

Feedback on the way I describe the project or how I could reach out to more potential contributors would also be very appreciated.

cheers,
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ryao
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PostPosted: Sun Oct 06, 2013 6:56 am    Post subject: Re: Neuroscience on Gentoo Reply with quote

Chymera wrote:
Hi guys, I have recently started writing ebuilds for some very important software packages used in brain imaging analysis. The ones NOT in the gentoo-science overlay are as follows:

- SPM ( 8 ) https://github.com/gentoo-science/sci/pull/107
- FSL https://github.com/TheChymera/sci/blob/fsl/sci-biology/fsl/fsl-5.0.4.ebuild (no pull request yet)
- AFNI https://github.com/gentoo-science/sci/pull/115

I have been working on these ebuilds for around 3 weeks, and it really seems I've exhausted my ebuilding knowledge. I have learned a lot in this time, but I seem to notice how the amount of time I can invest in this isn't enough to get things working in the foreseeable future.

I'd like to ask any of you if you would think it worthwhile to have these software packages on Gentoo (I am sure there are other neuroscientists except me using this fabulous distribution, and if there aren't we should take care of attracting them) - and if you would be willing to lend a helping hand.

I'm not asking you to finish my work for me, I'll still do whatever I can do on a daily basis - it's just that me + occasionally 2 gentoo-science devs doesn't seem to get this done.

Many Thanks,


I posted some comments here:

https://github.com/gentoo-science/sci/pull/107#issuecomment-25763360

Those will probably apply to your endeavors with other ebuilds as well. You would probably get more frequent help/attention from Gentoo developers in #gentoo-dev-help on freenode; additionally, the science team is available in #gentoo-science on freenode. There is also documentation on ebuild development available that you would probably find helpful:

http://devmanual.gentoo.org/
http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=1
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lledu
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PostPosted: Mon Nov 18, 2013 3:23 pm    Post subject: Reply with quote

Hi, I'm new in Gentoo and I'm also in the Neuroscience research field. I have a little question that how do you know the dependence of the FSL package? Like

Code:

COMMON_DEPEND="media-libs/glu
        media-libs/libpng
        media-libs/gd
        sys-libs/zlib
        dev-libs/boost
        "


I mean I find the manual in the FSL webpage which says FSL depends on ITK, VTK and so forth. So the ebuild file just did not reflect the whole dependence and how it work well?
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PostPosted: Mon Jan 20, 2014 6:25 pm    Post subject: Re: Neuroscience on Gentoo Reply with quote

Chymera wrote:
Hi guys, I have recently started writing ebuilds for some very important software packages used in brain imaging analysis. The ones NOT in the gentoo-science overlay are as follows:

- SPM ( 8 ) https://github.com/gentoo-science/sci/pull/107
- FSL https://github.com/TheChymera/sci/blob/fsl/sci-biology/fsl/fsl-5.0.4.ebuild (no pull request yet)
- AFNI https://github.com/gentoo-science/sci/pull/115

I have been working on these ebuilds for around 3 weeks, and it really seems I've exhausted my ebuilding knowledge. I have learned a lot in this time, but I seem to notice how the amount of time I can invest in this isn't enough to get things working in the foreseeable future.

I'd like to ask any of you if you would think it worthwhile to have these software packages on Gentoo (I am sure there are other neuroscientists except me using this fabulous distribution, and if there aren't we should take care of attracting them) - and if you would be willing to lend a helping hand.

I'm not asking you to finish my work for me, I'll still do whatever I can do on a daily basis - it's just that me + occasionally 2 gentoo-science devs doesn't seem to get this done.

Many Thanks,


Chymera: assuming you are still monitoring these posts, I could be of some assistance. I have a bunch of neuroscience/medical imaging ebuilds on my local systems that I could contribute, including:

fsl-5-0-5
freesurfer
imagej
dicom3tools
mitools

etc., which seem to "work" on my boxes, but of course I haven't really tested them on others. (fsl was a real pain to get working as I recall). I could distribute them on the github server if you like?
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Chymera
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PostPosted: Mon Feb 24, 2014 9:54 pm    Post subject: Reply with quote

@lledu:

Sadly, the FSL ebuild does not yet "work well". Does it work well on your machine? It emerged without issues and you can run it?

As the initial post in this this thread suggests, the expertise needed for the workload has slowly exceeded my capabilities, so if you would like to read through our FSL thread and see if there's anything in trhe ebuild you could patch, that would be awesome!

Regarding the deps, you may have missed this:
Code:

RDEPEND="${COMMON_DEPEND}
   dev-lang/tcl
   dev-lang/tk
   "


We have added all the deps which we could find, if you found something which is really missing, go ahead and make that change and submit a pull request to my repo!

@linux slacker:

That is awesome news! Indeed I'm here a lot less than I should be - but mostly because the activity seems to have dwindled these past 3 months. It'S really nice you came along. Are you on GitHub? If so just submit pull requests directly to the science overlay and add an @ reference in the text so that it shows up on my notifications (@TheChymera).
I'd be happy to lend a hand, and both me and @kiwifb would be grateful for some fresh input on the FSL build!
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