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16 Commits

Author SHA1 Message Date
Adam J. Stewart
2264e30d99
Update URL parsing regexes and tests (#13411) 
* Update URL parsing regexes and tests

* Get rid of no longer used README

* Merge py-udunits and py-cf-units

* netcdf -> netcdf-c

* setup_environment -> setup_*_environment

* Fix doc tests

* Few last minute fixes

* Simplify prefix removal copypasta
 2019-10-28 20:27:54 -05:00
Todd Gamblin
62927654dd checksums: use sha256 checksums everywhere 
We'd like to use a consistent checksum scheme everywhere so that we can:

    a) incorporate archive checksums into our specs and have a
       consistent hashing algorithm across all specs.

    b) index mirrors with a consistent type of checksum, and not one that
       is dependent on how spack packages are written.

- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
 2019-10-12 07:19:43 -07:00
Glenn P Johnson
b046ee20f5 Fixes for augustus package 
- add missing perl dependency
- only filter Makefile if referred to dependency is in the spec
- rewrite the shebang line of scripts to use spack perl
- remove tabix dependency as tabix and bgzip are part of htslib
 2019-09-13 19:07:35 -07:00
Justin Stanley
478c3f5e8b augustus: fix bam2wig auxprog build (#10362) 
* augustus: fix bam2wig auxprog build

* augustus: few more changes to make new versions work
 2019-02-04 10:36:10 -06:00
Todd Gamblin
6f50cd52ed copyright: update license headers for 2013-2019 copyright. 2019-01-01 00:44:28 -08:00
Todd Gamblin
eea786f4e8 relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers 
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
  - core and most packages are (Apache-2.0 OR MIT)
  - a very small number of remaining packages are LGPL-2.1-only
 2018-10-17 14:42:06 -07:00
Roberto Villegas-Díaz
8a35687d31 Augustus updated to version 3.3.1 (#8588) 
* Augustus updated to version 3.3.1

* Augustus - Version-specific URLs replaced by list_url

* Augustus - Adding tool versions back
 2018-07-22 17:11:37 -05:00
Todd Gamblin
54f97d1dec
Update copyright on LLNL files for 2018. (#7592) 2018-03-24 12:13:52 -07:00
Levi Baber
3945b2adb4 Augustus hash (#7447) 
* augustus: 3.3 package hash changed

* augustus: bamtools libraries now seem to be in lib64

* augustus: fix lib problem with older bamtools
 2018-03-09 16:05:39 -08:00
Levi Baber
12a670a556 Augustus update hash (#7286) 
* augustus: 3.3 package hash changed

* augustus: bamtools libraries now seem to be in lib64
 2018-02-19 22:06:40 -08:00
Levi Baber
08ea9808c6 adding specific version url for augustus 3.3 due to old folder structure (#6813) 2018-01-02 19:24:28 -06:00
Todd Gamblin
05fa302655
Replace github.com/llnl/spack with github.com/spack/spack (#6142) 
We moved to a new GitHub org! Now make the code and docs reflect that.
 2017-11-04 17:08:04 -07:00
Audrey Thoma
9326925d45 augustus: url fix (#5311) 2017-09-16 10:20:42 +02:00
Michael Kuhn
84ae7872d3 Update copyright notices for 2017 (#5295) 2017-09-06 17:44:16 -10:00
Audrey Thoma
2f29e9c18e braker & genemark-et: new packages (#5058) 
* braker & genemark-et: new packages

* fixing install
 2017-08-10 20:04:37 -05:00
Audrey Thoma
8125780b86 New package augustus (#4586) 
* augustus: adding augustus

* augustus: fixing flake8 things

* augustus: simplifying verbose
 2017-06-22 16:00:43 -05:00