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* dev-util/Tensile: move to standard directories.Benda Xu2021-02-076-3/+231
| | | | | | | | | | | Let cmake to be able to locate Tensile. Move source code out of the python site-packages tree. Reported-by: Yiyang Wu <xgreenlandforwyy@gmail.com>, Alexey Chernov Closes: https://bugs.gentoo.org/768474 Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* net-misc/cernbox-client: Bump to 2.7.5.3180.Oliver Freyermuth2021-02-062-0/+97
| | | | | | | | | Follows new version of net-misc/owncloud-client. Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Oliver Freyermuth <o.freyermuth@googlemail.com> Closes: https://github.com/gentoo/sci/pull/1051 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/quicktree: version bump to 2.5Aisha Tammy2021-02-052-0/+32
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
* sci-biology/open-ephys-gui: New packageThawann Malfatti2021-02-058-0/+297
| | | | | | | | | | | | | | | | Add static version and fix use of jack flag Move KEYWORDS to the if statement Fix extra blank lines and spaces as tab Fix dependencies Fix wrong package name in SRC_URI Add QA_PREBUILD and QA_PRESTRIPPED files Fix relative paths Fix wrong conditional flag statement Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: T Malfatti <malfatti@disroot.org> Closes: https://github.com/gentoo/sci/pull/966 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/ABI-connectivity-data: update homepageAndrew Ammerlaan2021-02-052-4/+4
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/act-bin: use httpsAndrew Ammerlaan2021-02-051-1/+1
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/bx-python: update homepageAndrew Ammerlaan2021-02-052-3/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/CAT: update homepageAndrew Ammerlaan2021-02-051-5/+3
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-libs/cs-rosetta-db: use httpsAndrew Ammerlaan2021-02-051-9/+9
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/erpin: update homepageAndrew Ammerlaan2021-02-051-2/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-chemistry/ligplot+: use httpsAndrew Ammerlaan2021-02-051-1/+1
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-chemistry/mics: use httpsAndrew Ammerlaan2021-02-051-3/+3
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-chemistry/nmrview: update homepageAndrew Ammerlaan2021-02-051-2/+2
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/quicktree: update homepageAndrew Ammerlaan2021-02-051-2/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/scan_for_matches: use httpsAndrew Ammerlaan2021-02-051-2/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/ssaha2-bin: update homepageAndrew Ammerlaan2021-02-051-2/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/zmap: use https for homepageAndrew Ammerlaan2021-02-051-2/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* dev-python/protobuf-python: added missing fileHorea Christian2021-02-051-0/+22
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Horea Christian <chr@chymera.eu>
* dev-libs/protobuf: added missing fileHorea Christian2021-02-041-0/+1
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-libs/mesquite: update homepageAndrew Ammerlaan2021-02-041-2/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* licenses: remove unused licensesAndrew Ammerlaan2021-02-043-194/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/sambamba: give tarball a proper nameAndrew Ammerlaan2021-02-042-2/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/polyphen: add bdep on unzipAndrew Ammerlaan2021-02-041-0/+1
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-physics/tauola: version bump, EAPI bumpAndrew Ammerlaan2021-02-045-110/+9
| | | | | | | | removed 9999, it is not doing anything, not inheriting git or defining SRC_URI Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/open-axiom: some steps towards fixing compilationAndrew Ammerlaan2021-02-041-3/+3
| | | | | | | now I get: ../interp/interpsys: No such file or directory Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-libs/jhdf5: version bump, EAPI bump, add keywordsAndrew Ammerlaan2021-02-043-27/+38
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-libs/htslib-plugins: version bump, EAPI bumpAndrew Ammerlaan2021-02-042-5/+4
| | | | | | | no keywords because dep iRODS doesn't have any Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-libs/blastdb: remove empty packAndrew Ammerlaan2021-02-042-34/+0
| | | | | | | only pulls in ncbi-tools++ and updates the blastdb nothing depends on this, hasn't been touched since 2014 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-chemistry/unio: remove pack, cannot fetchAndrew Ammerlaan2021-02-043-77/+0
| | | | | | HOMEPAGE gone, so cannot fetch SRC_URI of fetch RESTRICTed pack Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-chemistry/panav: add keywordAndrew Ammerlaan2021-02-041-1/+1
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-chemistry/jligand: EAPI bump, add keywordsAndrew Ammerlaan2021-02-041-8/+7
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/symap: version bump, EAIP bumpAndrew Ammerlaan2021-02-043-30/+41
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/stacks: version bump, EAPI bumpAndrew Ammerlaan2021-02-043-17/+99
| | | | | | | | does not install yet: access denied so no keywords for now Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/sra_sdk: call configure correctly for this packAndrew Ammerlaan2021-02-041-0/+6
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/snphylo: remove packAndrew Ammerlaan2021-02-043-48/+0
| | | | | | | | | | | | | | | | | | | | | | - this has missing deps - has not been fixed since it was added in 2015 - does not work, and will never work without some crazy workarounds. This package installs a script which looks for a config file and a directory named scripts in the same directory where the script is installed. At the moment only the master script is installed, which of course does not work because the config files and the .py files in the scripts dir are missing. We could of course add those, but then they would have to be in the same dir as the master script. (/opt would be an option, with a symlink of the executable script in a directory which is in PATH, though I am not sure if a symlink will work correctly with the way this package looks for it's config/scripts files) This was obviously designed for downloading and placing as is in some user directory. Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/sambamba: version bump, EAPI bumpAndrew Ammerlaan2021-02-044-33/+43
| | | | | | | | does not compile, seems to require some other compiler that is not packaged in ::gentoo at the moment Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/sailfish: fix configure phaseAndrew Ammerlaan2021-02-042-1/+13
| | | | | | | does not compile at the moment though so no keywords yet Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/roche454ace2caf: EAPI bumpAndrew Ammerlaan2021-02-031-8/+7
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/staden: fix configure phaseAndrew Ammerlaan2021-02-032-8/+8
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/staden_doc: add keywordsAndrew Ammerlaan2021-02-031-5/+7
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/caftools: EAPI bumpAndrew Ammerlaan2021-02-031-5/+6
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/prot4EST: EAPI bumpAndrew Ammerlaan2021-02-031-6/+6
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/prinseq-lite: EAPI bumpAndrew Ammerlaan2021-02-031-4/+3
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/primerD: fix some include statementsAndrew Ammerlaan2021-02-031-1/+13
| | | | | | | though it still does not compile Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/portrait: EAPI bumpAndrew Ammerlaan2021-02-031-3/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/polyphen: EAPI bump, fix configure, compile and installAndrew Ammerlaan2021-02-032-2/+38
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/pileup: EAPI bumpAndrew Ammerlaan2021-02-031-23/+18
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/phusion2: EAPI bump, add keywordsAndrew Ammerlaan2021-02-031-1/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* profiles/updates: move phusion to phusion2Andrew Ammerlaan2021-02-032-8/+5
| | | | | | and this time with the correct spelling Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/fusion: remove, duplicate of fusion2Andrew Ammerlaan2021-02-034-72/+1
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>