Commit Graph

18 Commits

Author SHA1 Message Date
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
Eric Martin
dc0b6a0613 samtools package: Add version 1.5 and htslib 1.5 dependency (#10825) 2019-03-11 19:29:29 -05:00
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
健美猞猁
7a5d54760e Add samtools 1.9 (#8961)
* Add smtools 1.9.

* Add hstlib 1.9.
2018-08-12 18:54:50 -05:00
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
David Orman
b5c02a2145 added htslib 1.7 and checksum (#7617) 2018-03-27 17:40:57 -05:00
Todd Gamblin
54f97d1dec
Update copyright on LLNL files for 2018. (#7592) 2018-03-24 12:13:52 -07:00
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
e69542c019 Fix tarball URL's for htslib (#5993)
A recent update (#5907) to htslib added a different URL for an old
version of htslib.

Now the package is using that URL as the pattern for the newer
versions too.

I have a vague memory of running into this before, that it's a known
issue.

This fixes it by adding an explicit `url_for_version` routine.
2017-10-30 22:49:52 -06:00
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
Todd Gamblin
cac4362f64 Make LICENSE recognizable by GitHub. (#4598) 2017-06-24 22:22:55 -07:00
Adam J. Stewart
745e2ce52f Fixes needed to build htop (#3691)
* Fixes needed to build htop

* Build libncursesw.so, not libncurses.so

* Remove htop hack now that it is picking up newer ncurses

* Tell packages to link to new ncursesw libraries
2017-04-05 16:03:11 -05:00
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
Adam J. Stewart
02f92fc7f8 Massive conversion from Package to AutotoolsPackage (#2845)
* Massive conversion from Package to AutotoolsPackage

* Forgot to convert p4est to AutotoolsPackage

* Fix typo

* Fix broken link in docs
2017-01-18 10:34:09 -08:00
George Hartzell
ef1369c365 Add package for htslib
Htslib was pulled out of samtools and made into a standalone thing.
This commit adds a packag for it, in support of the samtools package.
2016-08-04 14:18:03 -04:00