Commit Graph

19 Commits

Author SHA1 Message Date
Glenn Johnson
9f6ac938b7 Update and fix bcftools package (#14505)
* Update and fix bcftools package

This PR updates bcftools to 1.10.2 and is dependent on PR #14504.

This PR also fixes builds of other versions. Versions 1.2-1.4 did not
use autotools so when the packaeg was converted to use autotools with
version 1.6 those older versions could no longer build. Also, those
versions needed to be patched to use an external htsllib. The method of
finding the external htslib is also different for those older versions.

In addition, this PR adds two variants to bcftools:

- libgsl
- perl-filters

Finally, dependencies for perl and python are added, and an unused
dependency for libzip was removed.

* Do not use '@' in variant description

The '@' character in a variant description will cause a problem with
`spack info`.

```
==> Error: Incomplete color format: '@' in
expressions, for @1.8:
```

* Fix error with python2 processing this package
2020-01-14 22:04:47 -06:00
Todd Gamblin
4af6303086
copyright: update copyright dates for 2020 (#14328) 2019-12-30 22:36:56 -08:00
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
Ricardo Silva
3fc8203b93 bcftools: do not use bundled htslib (#10445)
* if the path to htslib is not specified the bundled one is built instead
* additionally this fixes the build with the intel compiler
2019-01-26 16:21:04 +01:00
Todd Gamblin
6f50cd52ed copyright: update license headers for 2013-2019 copyright. 2019-01-01 00:44:28 -08:00
Justin Stanley
d048bbb7ee bcftools: add version 1.9 (#9595) 2018-10-19 17:30:52 -07:00
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
健美猫
c53541e448 Bump samtools, hstlib and bcftools to version 1.8. (#8020)
* Bump samtools and hstlib to version 1.8.

* rm .bak.

* Bump bcftools to 1.8.

* bcftools@1.8 depends on libzip.
2018-05-04 16:27:54 -05:00
Levi Baber
dfc4a2aef1 bcftools: new version (#7930) 2018-04-26 22:48:01 -05:00
Todd Gamblin
54f97d1dec
Update copyright on LLNL files for 2018. (#7592) 2018-03-24 12:13:52 -07:00
健美猫
b733ce1e5f bcftools is a AutotoolsPackage. (#6881) 2018-01-10 09:45:05 -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
George Hartzell
ff031de800 Add old version to bcftools (#5907)
* bcftools v1.2 and htslib v1.2

* dependency change - only require dependencies for v1.2
2017-10-25 12:20:42 +02:00
Carlos Bederián
db149876a4 samtools: add version 1.6 + some fixes (#5715)
* htslib: add version 1.6

* samtools: add version 1.6, remove zlib dependency

* bcftools: add version 1.6, switch to using standalone htslib
2017-10-12 10:08:31 -06:00
Michael Kuhn
84ae7872d3 Update copyright notices for 2017 (#5295) 2017-09-06 17:44:16 -10:00
Audrey Thoma
3eedbd7c4e py-deeptools: new package and dependencies (#4717)
* py-deeptools: new package and dependencies

* py-deeptools: fixing python things

* missed a fix
2017-07-13 22:02:08 -05:00
Todd Gamblin
cac4362f64 Make LICENSE recognizable by GitHub. (#4598) 2017-06-24 22:22:55 -07:00
George Hartzell
d6cbae81c7 Update/samtools (#3595)
* Update samtools family to 1.4

* simple cleanup

* Make bzip depends_on for future versions too
2017-03-28 21:34:41 -05:00
George Hartzell
fd11db92e1 Add package for bcftools 2016-08-04 14:18:03 -04:00