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Author SHA1 Message Date
Todd Gamblin
37fc258313 Remove vestigial methods from Package. 2016-08-08 21:04:23 -07:00
Todd Gamblin
faa0a0e4c3 Add a ProviderIndex cache. 
- Spack will check if the index needs updating, and will only parse
  all package files if it does.

- Spack tries to parse as few package files as necessary.
 2016-08-08 21:04:23 -07:00
Todd Gamblin
cf2f902b82 Make ProviderIndexes mergeable, so we can cache them per-repo. 2016-08-08 21:04:23 -07:00
Todd Gamblin
bf028990e7 Make ProviderIndex yaml-izable. 
- allow a provider index to be stored and re-read.
 2016-08-08 21:04:23 -07:00
Todd Gamblin
025609c63f More compact YAML formatting for abstract specs. 
- Don't add empty/absent fields to Spec YAML when they're not there.
 2016-08-08 21:04:23 -07:00
Todd Gamblin
7aaad89ba9 Lazily evaluate all_package_names in repository.py 
- Don't need to list all packages unless we have to.

- Only use the list of all packages for existence checks if we have
  generated it for some other purpose.
 2016-08-08 21:04:23 -07:00
becker33
2b94d7cf8e Merge pull request #1472 from adamjstewart/fixes/rstrip 
Only strip newline chars, not spaces
 2016-08-08 13:28:56 -07:00
Adam J. Stewart
5d48c108a3 Only strip newline chars, not spaces 2016-08-08 15:02:05 -05:00
becker33
3ea1325620 Merge pull request #1345 from hartzell/feature/add-perl-dependency-to-git 
Add depends_on('perl'), depends_on('pcre') to git package
 2016-08-08 09:44:50 -07:00
Todd Gamblin
dd30066feb Merge pull request #1449 from hartzell/feature/add-package-for-prank 
Add package for prank and supporting tools
 2016-08-07 23:43:40 -07:00
Todd Gamblin
e65a8b6a9a Merge pull request #1463 from davydden/pkg/opium 
opium: add new package
 2016-08-07 15:56:27 -07:00
Todd Gamblin
8121ac2c27 Merge pull request #1464 from hartzell/feature/update-lmod 
No need to patch Lmod after 6.4.4
 2016-08-07 15:55:16 -07:00
Todd Gamblin
93f5a750cb Merge pull request #1465 from glennpj/pango_url 
Add list_url to pango package
 2016-08-07 15:55:04 -07:00
Todd Gamblin
281f6f18e1 Merge pull request #1466 from pramodk/develop 
PDT should download full installer package
 2016-08-07 15:54:50 -07:00
Denis Davydov
db87a9d3ce tar: fix 1.28 on macOS; add 1.29 (#1462) 2016-08-07 15:54:01 -07:00
Adam J. Stewart
d7329d7bc2 Fix erroneously stripped trailing whitespace in patch (#1467) 2016-08-07 15:53:25 -07:00
Pramod Kumbhar
e9edfec0ec PDT should download full installer package pdtoolkit-X.tar.gz (default pdt-X.tar.gz is only for x86 and cray) 2016-08-07 01:14:26 +02:00
Glenn Johnson
2ad21e7070 Add list_url to pango package 
Added a `list_url` so the updated pango tar file can be retrieved.
 2016-08-06 18:12:47 -05:00
George Hartzell
09d96bef9f No need to patch Lmod after 6.4.4 
The Lmod author changed the src so that it uses the tclsh (and shared
libraries) discovered at configure time.  He did it differently that I
did in this patch, but he changes solve our problem too, so...
 2016-08-06 17:39:05 -04:00
George Hartzell
9ebbde0e01 Make configure use our gettext library 
The configure script needs extra encouragement to link against our
gettext/libintl library.
 2016-08-06 16:28:47 -04:00
George Hartzell
1de5817b58 Clean up rebase problems 
My rebase duplicated the depends_on('zlib') and dropped the --with-curl
from the configure.

This fixes those.
 2016-08-06 16:28:47 -04:00
George Hartzell
f699d7c08e [Whitespace] Gather the depends_on's together. 2016-08-06 16:28:47 -04:00
George Hartzell
152fa33a55 Call configure --with-libpcre=... to use our pcre 
An earlier commit claimed that this package depends_on('pcre') but I
didn't fix the call to configure that enabled it.

This fixes that.
 2016-08-06 16:28:47 -04:00
George Hartzell
3cf2fd40a8 Enable depends_on('pcre') also 
While I have the patient on the operating table, @adamjstewart asked
me to uncomment and test the depends_on('pcre').

Did it and it Works For Me(tm).
 2016-08-06 16:28:47 -04:00
George Hartzell
653905e3a2 Add depends_on('perl') to git package 
This commit changes the git package to depend_on('perl').  The system
perl is not always sufficient to install git (e.g. a CentOS7 system with
the development tools group installed has perl but not the
ExtUtils::MakeMaker package that git needs) and one can't always update
the system's perl.

This PR depends_on PR #1339, which adds a perl package to spack.
 2016-08-06 16:28:47 -04:00
George Hartzell
f800708ef3 Switch to using *std_cmake_args 2016-08-06 16:27:40 -04:00
George Hartzell
6a62a6b693 Flake8 whitespace cleanup 2016-08-06 16:27:40 -04:00
George Hartzell
a07a0ef54b Add Bio++ tool suite and supporting libs 
Add the Bio++ suite and its supporting libraries.
 2016-08-06 16:27:40 -04:00
George Hartzell
3c81bb44ba Add package for mafft 2016-08-06 16:27:40 -04:00
George Hartzell
e0db1f0268 Add package for exonerate 2016-08-06 16:27:40 -04:00
George Hartzell
9e16902397 Fix name of bpp-suite (missing -...) 2016-08-06 16:27:40 -04:00
George Hartzell
63592096c5 Add package for prank 2016-08-06 16:27:40 -04:00
Denis Davydov
4983ebcf7c opium: add new package 2016-08-06 21:35:52 +02:00
becker33
d3f115933e Merge pull request #1451 from hartzell/feature/add-package-for-fastx_toolkit 
Add package for fastx toolkit
 2016-08-05 15:09:46 -07:00
becker33
18d155e713 Merge pull request #1452 from hartzell/feature/add-package-for-samtools 
Add package for samtools
 2016-08-05 15:09:41 -07:00
George Hartzell
a6afaeb974 Remove lingering FIXME commentary 2016-08-05 17:51:24 -04:00
George Hartzell
769408130a Samtools depends on htslib from 1.3.1 onward 
Samtools used to (before 1.3.1) include it's own copy of htslib.  Going
forward, it needs to use the standalone htslib.
 2016-08-05 17:47:11 -04:00
becker33
90f68d2c66 Merge pull request #1460 from glennpj/fix_list_vcs 
Catch error for version in VCS
 2016-08-05 13:34:37 -07:00
becker33
8e20a14945 Merge pull request #1453 from hartzell/feature/add-package-for-seqtk 
Add package for seqtk
 2016-08-05 10:25:19 -07:00
becker33
f403f256ca Merge pull request #1450 from hartzell/feature/add-package-for-bwa 
Add package for bwa
 2016-08-05 10:21:10 -07:00
Glenn Johnson
20221ee3aa Catch error for version in VCS 
This PR will catch the error where the url can not be determined from a
VCS URL, such as git. It will print a message to the console and move on
because it should not be a fatal error at this point in the process.

This should fix #1459.
 2016-08-05 11:16:43 -05:00
becker33
594a6710ed Merge pull request #1442 from suraia/update-scorep-2.0 
Update Score-P to 2.0

Most likely this can be generalized to link against older versions of dependencies, but it looks good for now.
 2016-08-05 08:57:25 -07:00
George Hartzell
d6dedee6ff Flake8 cleanup 2016-08-04 15:23:04 -04:00
Bruno Turcksin
0c02ee86a7 Add Trilinos 12.6.4 (#1447) 2016-08-04 11:29:10 -07:00
George Hartzell
e12d7aadda Add package for seqtk 
Seqtk is a tool for working with fast[aq] files.
 2016-08-04 14:18:03 -04:00
George Hartzell
fd11db92e1 Add package for bcftools 2016-08-04 14:18:03 -04:00
George Hartzell
ba0577dc96 Update samtools to support v1.3.1 
Update the samtools package to support v1.3.1, which
- now uses configure script; and
- now depends on external htslib package.

The dependency on mpc seems to have been bogus, it's never linked in,
nor is it mentioned in the source tree.  I *do* have a version in
/usr/lib64, but ldd does not sure it being linked in either....

By depending on 'ncurses' I can do away with the need for the patch.
 2016-08-04 14:18:03 -04:00
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
George Hartzell
e17862c421 Add package for fastx toolkit 
Tools for working with FASTA/FASTQ files.
 2016-08-04 14:18:02 -04:00
George Hartzell
d5bb2955b1 Add package for libgtextutils 
Gordon's Text utils Library, in support of fastx toolkit.
 2016-08-04 14:18:02 -04:00