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Andrew Ammerlaan 1c4f022505
sci-biology/fsl: add version 6.0.4
Closes: https://github.com/gentoo/sci/pull/1074
Co-authored-by: Paul Polak <paul.polak@med-image.info>
Package-Manager: Portage-3.0.20, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
2021-07-18 12:47:25 +02:00
.github/workflows .github/workflows: always use the latest version of repoman 2021-04-02 12:04:44 +02:00
app-arch/libdeflate app-arch/libdeflate: version bump to 1.7 2021-03-01 13:14:23 +00:00
app-office/visidata app-office/visidata: eutils --> optfeature 2021-05-08 16:28:50 +02:00
app-text/noweb app-text/zotero-bin: move to ::gentoo 2021-05-22 13:04:26 +02:00
app-vim/vim-gromacs app-vim/vim-gromacs: remove RedundantLongDescription 2021-03-03 16:15:21 +01:00
dev-cpp dev-cpp/blitz: drop replaced blitz-1.0.2_p20200524.ebuild 2021-04-20 11:44:15 -04:00
dev-java dev-java/netcdf: remove last-rited package 2021-06-01 11:18:06 +02:00
dev-lang dev-lang/conceptual: bump PYTHON_COMPAT 2021-06-01 10:45:12 +02:00
dev-libs dev-libs/optix: bump to 7.2.0 2021-07-03 12:55:11 +02:00
dev-ml/lacaml dev-ml/lacaml: add missing dep 2021-05-25 20:13:20 +02:00
dev-perl dev-perl/BTLib: add blocker 2021-05-25 13:18:02 +02:00
dev-python dev-python/cadquery-pywrap: add 2021-07-18 10:34:45 +02:00
dev-tcltk/togl dev-tcltk/togl: EAPI bump 2021-03-03 16:04:13 +01:00
dev-util dev-util/rocm-clang-ocl: add 4.1.0 2021-04-05 18:41:35 +02:00
docs virtual/{{c,}blas,lapack{,e}}: replaced by counterparts in ::gentoo. 2019-08-08 09:20:00 +08:00
eclass eclass/numeric-int64-multibuild.eclass: fix @ECLASS variable 2021-01-30 16:24:33 +01:00
licenses licenses/netCDF: remove unused license 2021-07-03 12:20:46 +02:00
media-gfx/brlcad media-gfx/brlcad: add missing slash 2021-01-24 12:48:15 +01:00
media-libs media-libs/libgfx: Remove test use flag 2021-06-05 14:38:26 +02:00
metadata metadata/layout.conf: ban EAPI 5 2021-03-20 11:42:41 +01:00
net-misc/cernbox-client net-misc/cernbox-client: Drop old version. 2021-06-05 20:55:16 +02:00
profiles sys-kernel/dkms: remove last-rited pack 2021-07-14 21:48:15 +02:00
sci-astronomy sci-astronomy/wcslib: landed on to ::gentoo. 2020-11-09 15:07:01 +08:00
sci-biology sci-biology/fsl: add version 6.0.4 2021-07-18 12:47:25 +02:00
sci-chemistry sci-chemistry/MotionCor2: fix cuda flag 2021-06-01 10:59:34 +02:00
sci-electronics/minipro sci-electronics/tnt: drop dead package 2020-09-26 17:26:58 +00:00
sci-libs sci-libs/ciftilib: fixed boost version checking 2021-06-22 19:44:08 -04:00
sci-mathematics sci-mathematics/gappa: add version 1.4.0 2021-06-09 16:25:16 +02:00
sci-misc sci-misc/praat: version bump 6.1.42 2021-05-08 15:50:57 +02:00
sci-physics sci-physics/genfit: fix MultipleKeywordsLines 2021-03-20 12:02:56 +01:00
sci-visualization sci-visualization/scidavis: move to ::gentoo 2021-05-23 13:25:16 +02:00
scripts scripts/setup-and-run-repoman.sh: checkout portage tag 2021-06-17 08:43:28 +02:00
sys-apps/ndctl sys-apps/ndctl: drop old version 2020-12-23 02:09:21 +00:00
sys-cluster/modules sys-cluster/lmod: lmod is now in ::gentoo 2021-02-14 11:55:01 +00:00
virtual/scalapack virtual/blacs: remove obsolete virtual 2021-01-05 19:10:00 +01:00
x11-libs/xview-bin x11-libs/qwtplot3d: move to ::gentoo 2021-05-23 13:24:28 +02:00
x11-misc/envytools x11-misc/envytools: remove duplicate inherit of git-r3 2021-01-30 16:40:46 +01:00
.gitignore profiles: remove use.local.desc permanently 2017-10-15 17:06:39 -07:00
CONTRIBUTING.md CONTRIBUTING.md: update accepted EAPIs 2021-03-20 11:42:18 +01:00
README.md README.md: freenode --> libera 2021-06-20 15:11:59 +02:00


The Gentoo Science Project Repository

pkgcheck repoman contributions welcome chat on libera

This is an official mirror of the Gentoo Science ebuild repository, containing numerous scientific software packages.

See Project:Science for more information on the project.


  1. Installation
  1. Usage
  2. Contributing


Eselect-repository install

The easiest way to enable the overlay is to:

emerge --noreplace eselect-repository && eselect repository enable science && emerge --sync

and emerge the package as usual.

Manual Install

As per the current Portage specifications, ebuild repositories (a.k.a. overlays) can be managed via file collections under /etc/portage/repos.conf/, via the new plug-in sync system.

To enable the overlay without the need for additional software, you first need to have git installed:

emerge --ask --verbose dev-vcs/git

Then you need to add the science repository configuration by downloading the science.conf file:

wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
	-O /etc/portage/repos.conf/science

Manual Uninstall

To uninstall the overlay, simply run:

rm /etc/portage/repos.conf/science
rm /var/db/repos/science -rf

Layman Install

You can also install the overlay via the layman overlay manager.

emerge --ask --verbose app-portage/layman
layman --add science

Layman Uninstall

To delete the overlay, run:

layman --delete science

Using Packages from ::science

To start using the overlay you now only need to get the newest files, via:

emerge --sync science

To be able to install ::science packages you need to make sure that you are accepting the ~${ARCH} keyword for your respective architecture. This may already be the case globally on your system, and you can check whether this is the case by running:

grep "~$(portageq envvar ARCH)" /etc/portage/make.conf

If the above returns empty, you will need to instruct Portage to accept ~${ARCH} packages.

This can be done for ::science specifically:

mkdir -p /etc/portage/package.accept_keywords
printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords/science

If the above fails with mkdir: cannot create directory /etc/portage/package.accept_keywords: File exists this means you are using a file and not a directory, and you can instead run:

printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords

Alternatively, and only if you know what you are doing, you can accept ~${ARCH} packages globally:

printf 'ACCEPT_KEYWORDS="~%s"' "$(portageq envvar ARCH)" >> /etc/portage/make.conf

The downside of this approach is potentially higher instability, the advantage is that often ::science packages require ~${ARCH} packages from ::gentoo as well.


If you fork, we will merge!
We welcome new contributors and are happy to include new packages.

Areas to contribute

find . -type f -name "*.ebuild" ! \( -wholename "*.git*" -o -wholename "*profile*" -o -wholename "*metadata*" \) | while read ff; do grep -lRE "EAPI.*6" /dev/null $ff; done


For a brief introduction please see our contributing guide. Further helpful resources are:

Additionally, please make sure to add the Science Project as an additional maintainer to any new packages you submit. For an example, take a look at the metadata for the Numba package - dev-python/numba/metadata.xml


You can ask for help on Libera IRC in #gentoo-science. Alternatively you can report bugs on the GitHub issues page.