Syzygial/ccpkgs
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cc-20.09
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Author SHA1 Message Date
Tyson Whitehead
bcbb1ef4fb sambamba: Upgrade to 0.6.7 and compile with upstream ldc 
Fixes new compilation issues with tupple operator being dropped
 2018-06-27 14:19:23 -04:00
Tyson Whitehead
c72ea282b4 blast: Requires previous version of boost 2018-06-25 15:48:08 -04:00
Tyson Whitehead
01a6ed3f22 nix: Update patches for 2.0 
* Drop stat patch as was accepted upstream.
* NIX_REMOTE scheme is now URI based tcp://host:port
 2018-06-25 15:45:44 -04:00
Armin Sobhani
fde6c31445 add idba bioinformatics package 2018-06-25 15:38:22 -04:00
Tyson Whitehead
9ebec6056b Set SKIP_CC_CVMFS=1 in nix-shell pure mode to avoid CVMFS pollution 2018-04-25 14:07:28 -04:00
Tyson Whitehead
b3a150a471 blast: Package official ncbi-blast package 
Based on initial work by Armin.
 2018-04-24 16:46:55 -04:00
Tyson Whitehead
1c1f16a2b3 octopus: Switch to new version structure 2018-02-07 13:39:27 -05:00
Tyson Whitehead
bb7076d9f0 openfoam: Update hash and re-enable 2018-02-07 13:38:09 -05:00
Tyson Whitehead
159a3a8c0d README: Note commit message package: ... convention 2018-02-07 10:39:22 -05:00
Tyson Whitehead
7ec0d48784 README: Gabled sentance on entering nix-shell environments 2018-02-07 10:37:09 -05:00
Tyson Whitehead
6f98376d7f README: Line break in inline code messes up rendering 2018-02-07 10:36:28 -05:00
Tyson Whitehead
33be90dd1e README: The nix-env --install --attr needs the channel prefix 2018-02-07 10:36:14 -05:00
Tyson Whitehead
be9d77db0f README: Note that the nix module has to be loaded 2018-02-07 10:34:55 -05:00
Tyson Whitehead
6cb654e501 octopus: Initial packaging 2018-02-06 22:10:02 -05:00
Tyson Whitehead
e5a284589c README: Minor clarifications and cleanups 2018-02-06 15:20:33 -05:00
Tyson Whitehead
88de1da361 Rewrite of README for new overlay framework 2018-02-05 17:46:35 -05:00
Tyson Whitehead
1cb8792d05 Missing toString caused nixpkgs import if not using ./upstream 2018-01-30 11:58:38 -05:00
Tyson Whitehead
86b95e8349 Forgot to wind super through attribute queries for hydra in 1d156fc 2018-01-24 10:05:26 -05:00
Tyson Whitehead
06801cb4f0 temporary: nix: Work around for broken stat size #1645 2018-01-23 23:52:14 -05:00
Tyson Whitehead
820719fb02 nix: Patch to support NIX_DAEMON=<addr>:<port> 2018-01-23 23:46:45 -05:00
Tyson Whitehead
1d156fc470 Make super available in all-*.nix for override* use 2018-01-23 23:37:03 -05:00
Tyson Whitehead
39f4271d28 Tested hydra job to control release of channel (has to build okay) 2018-01-23 22:57:09 -05:00
Tyson Whitehead
c0ba1362eb Combine ccpkgs and nixpkgs versions together in suffix 
Want a unique name for the output product of each combination for
the channel-update code.
 2018-01-23 18:56:11 -05:00
Tyson Whitehead
e1171b5ed1 firedrake meraculous openfoam sumo: Disable broken packages 2018-01-20 15:30:12 -05:00
Tyson Whitehead
1825738822 sambamba: Add package from asobhani/nix-bioinfo-pkgs-sharcnet 2018-01-19 12:08:53 -05:00
Tyson Whitehead
30dbd204e7 Include hydra targets for contained pkgs and temporaries 2018-01-19 04:17:57 -05:00
Tyson Whitehead
8b85483c50 Add release code for building channel (drop nixpkgs submodule) 
Decided it would be best if hydra just provided the latest stable
nixpkgs for us to use.  This way there is no need for an udpate
script that polutes our logs with update submodule commits.
 2018-01-19 03:40:19 -05:00
Tyson Whitehead
b3f97768e9 temporary: Add separate space for temporary overlays 
These are intended for temporary fixes to upstream that are
expected to be dropped when incorporated in upstream.
 2018-01-19 02:15:00 -05:00
Tyson Whitehead
cc3de0d5a8 nltk: Now in upstream 2018-01-19 02:15:00 -05:00
Tyson Whitehead
38d4b97ead namd: Convert to new overlay system 2018-01-19 02:14:59 -05:00
Tyson Whitehead
e44edd0230 sumo: Convert to new overlay system 2018-01-19 02:14:59 -05:00
Tyson Whitehead
fa856eb582 openslide: Convert to new overlay system 2018-01-19 02:14:59 -05:00
Tyson Whitehead
ad0a5b2336 openfoam: Convert to new overlay system 2018-01-19 02:14:59 -05:00
Tyson Whitehead
99a331d613 meraculous: Convert to new overlay system 2018-01-18 01:00:03 -05:00
Tyson Whitehead
8dda256fad firedrake: Moved to new overlay system and shared sub-scope 
Firedrake contains a ton of inter-connected dependencies, many of
which are either firedrake specific or forked versions of upstream
packages.  Cleaner to create a firedrake sub-scope for all these.
 2018-01-18 00:59:30 -05:00
Tyson Whitehead
d4dd6ff700 cryptominisat: Convert to new overlays system 2018-01-18 00:58:53 -05:00
Tyson Whitehead
24255eab8d Overlays based framework for extending nixpkgs 2018-01-18 00:58:14 -05:00
Tyson Whitehead
a6b6045a5e Submodule to track upstream nixpkgs (nixpkgs-channel/nixos-17.09) 2018-01-18 00:05:04 -05:00
Tyson Whitehead
1316168a6d Add a bit about creating your own expressions 2018-01-14 10:00:19 -05:00
Tyson Whitehead
88833a0edd firedrake: Bump version snapshot to a967a34 2018-01-14 09:19:56 -05:00
Tyson Whitehead
572953ff66 firedrake: Add meta information 2018-01-14 09:19:03 -05:00
Tyson Whitehead
adbd06e5b2 Merge branch 'firedrake' into 'master' 
firedrake: Initial packaging



See merge request !4
 2017-05-01 20:38:50 -04:00
Tyson Whitehead
a2f7eda6de firedrake: Initial packaging 2017-05-01 20:09:09 -04:00
Tyson Whitehead
bcdbc895aa Merge branch 'openslide' into 'master' 
openslide: Initial packaging (includes python interface)

* Add upstream commit 4ea9211 for Pillow issue 2259

See merge request !3
 2017-05-01 17:48:55 -04:00
Tyson Whitehead
c979c0fe6b openslide: Initial packaging (includes python interface) 
* Add upstream commit 4ea9211 for Pillow issue 2259
 2017-05-01 17:40:26 -04:00
Tyson Whitehead
e0577fa54e Merge branch 'meraculous' into 'master' 
meraculous: Initial packaging

The example run given in the [manual](http://jgi.doe.gov/data-and-tools/meraculous) ran okay. The `use_cluster` setting (i.e., the one that causes the `run_meraculous.sh` script to try and submit jobs to the cluster) doesn't work as the default scripts assume [SGE](https://en.wikipedia.org/wiki/Oracle_Grid_Engine). Fixing that would require a lot of work.

See merge request !2
 2016-12-22 15:52:25 -05:00
Tyson Whitehead
ee64d3347c meraculous: Initial packaging 2016-12-22 15:44:49 -05:00
Tyson Whitehead
02dcc6b314 namd: Remove unneeded perl dependency 2016-11-28 14:36:37 -05:00
Tyson Whitehead
e2d17b0061 Merge remote-tracking branch 'namd/master' into namd 2016-11-28 14:09:42 -05:00
Tyson Whitehead
cbd2a47683 namd: Generalize of over specific version numbers 2016-11-28 13:54:44 -05:00