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Author SHA1 Message Date
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
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
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
George Hartzell
d4274b32f2 Make flake8 happy (long lines) 2016-08-04 14:18:01 -04:00
Michael Kuhn
d7665a63e3 flake8 fixes 2016-08-04 19:04:48 +02:00
becker33
1ac1cc3d2c Merge pull request #1437 from jgalarowicz/update-xercesc 
Update the version of xerces-c, where the developers remove the old v…
 2016-08-04 09:00:36 -07:00
becker33
3c6f6fc811 Merge pull request #1438 from jgalarowicz/update-libmonitor 
Update libmonitor to use its new github location, it does not exist w…
 2016-08-04 08:59:35 -07:00
becker33
cabcdf0ec9 Merge pull request #1443 from davydden/pkg/dealii_python 
dealii: add optional python bindings
 2016-08-04 08:43:36 -07:00
becker33
fcc8b1d3e4 Merge pull request #1431 from hartzell/feature/add-package-for-unison 
Add package for unison (and ocaml)
 2016-08-04 08:41:45 -07:00
Denis Davydov
af8741c23c dealii: add optional python bindings 2016-08-04 16:11:14 +02:00
Michael Kuhn
584e5506f2 Update Score-P to 2.0 2016-08-04 14:24:25 +02:00
Todd Gamblin
b7fa2c4e21 Fix #1429: Remove git dep from gettext; break circular dependency. 
- It's not really a circular dependency -- git is a run dependency of gettext

- We can revert this change when Spack is smart enough to make git a run
  dependency and build it.
 2016-08-03 21:53:53 -07:00
Jim Galarowicz
2e1dbd0697 Fix flake8 errors for: Update libmonitor to use its new github location, it does not exist where the package file now points to. 2016-08-03 21:32:15 -05:00
Jim Galarowicz
e69423a154 Fix flake8 errors for Update the version of xerces-c, where the developers remove the old version, so there is no fallback. 2016-08-03 21:28:56 -05:00
Jim Galarowicz
e68b7d8c63 Update libmonitor to use its new github location, it does not exist where the package file now points to. 2016-08-03 21:08:48 -05:00
Jim Galarowicz
638f779841 Update the version of xerces-c, where the developers remove the old version, so there is no fallback. 2016-08-03 21:04:17 -05:00
George Hartzell
43371c31a2 Flake8 cleanup 2016-08-03 16:51:53 -04:00
Todd Gamblin
dce105d16f Merge pull request #1382 from KineticTheory/gktplus3-deps 
GTK+3: Provide updates to package dependencies.
 2016-08-03 13:45:18 -07:00
George Hartzell
4acf6d76bf Add package for unison 
Add package for unison (the file synchronizer).

Needs the ocaml compiler to build.
 2016-08-03 16:41:31 -04:00
George Hartzell
a7bfaa3797 Add package for ocaml compiler 
Installs the ocaml compiler.
 2016-08-03 16:41:31 -04:00
Kelly (KT) Thompson
7c46a4c0e4 Provide minor updates after code review 
+ Always depend on the gettext package. This simplifies the logic and I no
  longer need to 'import sys'
+ Only apply the patch for the older version of glib.
 2016-08-03 13:26:02 -06:00
becker33
3e6ebd577f Merge pull request #1378 from LLNL/bugfix/gh-1324-intel-parallel-studio 
Bugfix/gh 1324 intel parallel studio
 2016-08-03 10:46:40 -07:00
becker33
353726f08f Merge pull request #1156 from adamjstewart/features/py-meep 
Add py-meep package and dependencies

Merging to add the gettext support, will submit a separate issue for the LD_LIBRARY_PATH issue with MPI and py-meep
 2016-08-03 10:07:05 -07:00
becker33
b9195b415a Merge pull request #1420 from epfl-scitas/packages/plumed 
plumed : added package
 2016-08-03 08:36:31 -07:00
alalazo
2f1c000f62 qa : flake8 issues 2016-08-03 08:26:58 +02:00
Kelly (KT) Thompson
d7d12aa2dc One more formatting change to make flake8 happy. 2016-08-02 19:05:48 -06:00
becker33
48997cffa1 Merge pull request #1233 from hartzell/add-nextflow 
First cut package for nextflow, has issues
 2016-08-02 11:52:19 -07:00
Denis Davydov
f90692cf81 arpack-ng: fix blas/lapack libraries 2016-08-02 20:27:34 +02:00
becker33
b5a117c923 Merge pull request #1366 from hartzell/feature/add-package-for-ack 
Add package for ack
 2016-08-02 10:11:11 -07:00
becker33
1534a115bd Merge pull request #1421 from hartzell/feature/add-package-for-texlive 
Add package for texlive
 2016-08-02 10:10:43 -07:00
becker33
a03a35565e Merge pull request #1339 from hartzell/features/add-perl 
Add perl package
 2016-08-02 10:10:04 -07:00
George Hartzell
fa70a837d4 Remove accidentally committed cabal-install bits 2016-08-02 13:00:47 -04:00
becker33
91004158c6 Merge pull request #1243 from davydden/pkg/atlas_urls 
atlas: fix urls and shared libs
 2016-08-02 09:59:05 -07:00
becker33
3f26bbc8b3 Merge pull request #864 from davydden/kdiff3 
kdiff3: initial version of the package
 2016-08-02 09:35:00 -07:00
becker33
a3322fab0a Merge pull request #1360 from glennpj/pysetuptoolsdep 
Add py-setuptools dependencies to packages
 2016-08-02 09:33:40 -07:00
becker33
21158195fb Merge pull request #1354 from paulhopkins/bugfix/preferred_variants_do_not_recognise_-variant 
Bugfix/preferred variants do not recognise  -variant
 2016-08-02 09:15:06 -07:00
George Hartzell
74a181febc Remove local copy of cpanm installer 
This is handled as a resource in the package now.
 2016-08-02 12:13:24 -04:00
George Hartzell
4c8672ed1f Add previous versions back into package 
Following the advice of @glennpj, added the old versions back into the
packages.

I can install the current packages and the previous packages.
 2016-08-02 11:45:16 -04:00
George Hartzell
c77425bb22 Remove useless def unpack 
Before I learned that I was stumbling over a real but (#1308), I thought
I needed to arrange for the fetcher to skip the unpack step.

This commit removes the useful `def unpack`.
 2016-08-02 11:32:19 -04:00
George Hartzell
a6605d842b Flake8 cleanup. 2016-08-02 11:25:03 -04:00
George Hartzell
f2f5f6c279 Touch up variant comment 2016-08-02 11:18:50 -04:00
George Hartzell
c994565c62 Use "resource" machinery to manage cpanm tarball 
Use the resource machinery to fetch/cache/unpack/... the App::cpanminus
tarball.

- this hardcodes the version, I can't figure out how to use a variant to
  hold/set the value and access it in the resource().
- change up the install to use the `with working_dir()` meme.
 2016-08-02 11:16:46 -04:00
George Hartzell
1b9becc541 Add the std spack header to perl/package.py 
Stole the example header from antlr/package.py, included it at the top
of perl/package.py.
 2016-08-02 11:16:46 -04:00
George Hartzell
08ff7b65af Make running perl's tests conditional 
Make running perl's tests conditional, one must now specify the
`--run-tests` flag to the `spack install` command in order to run the
tests.

On one system (8 core, 16GB Digital Ocean Droplet), installing without
tests takes 3 minutes, with tests takes 16 minutes.
 2016-08-02 11:16:46 -04:00
George Hartzell
4d72e0fb9d Make the cpanm version a variant 
Rather than hard-coding the verison of `cpanm` that's [optionally]
installed into the core, make it a variant with a default value of
'1.7042'.

Also discovered that `prefix + 'bin'` is the same as `prefix.bin`, so
embetter that bit of code.
 2016-08-02 11:16:46 -04:00
George Hartzell
a5a4525bed Add perl package 
Add perl package, based on [work by
justintoo](https://github.com/LLNL/spack/pull/105).  He had too many
things pulled into that pull request, this just adds a perl package.

Support the current releases on the past three minor branches.

Run perl's tests before installing.

Install cpanm into the core (makes building on top of this perl *much*
simpler).  Controlled by a variant.
 2016-08-02 11:16:46 -04:00
George Hartzell
949621eb7f Add package for texlive 2016-08-02 11:15:42 -04:00
George Hartzell
857a03c127 Ack should depends_on('perl') 
Add a depends_on('perl') and rewrite the script's `#!` line to refer to
that Perl's `perl` executable.
 2016-08-02 11:11:05 -04:00
George Hartzell
114da813a3 Remove unnecessary imports. 
Now that it's sporting a cleaner install method, these imports are
unnecessary.
 2016-08-02 11:11:05 -04:00
George Hartzell
bf467c5df3 Remove override of unpack(self) 
I cargo culted that from my *nextflow* package.  I [thought I] needed it
to work around Spack trying to use tar to unpack something that was
neither a tar ball nor unpackable.

This package works fine without it.  In retrospect, the error that I was
seeing in the *nextflow* package was probably this problem #1308.
 2016-08-02 11:11:05 -04:00
George Hartzell
6c3623422f Use cleaner mech to install script 
Use @adamjstewart's nicer bit of python code in the
install method.
 2016-08-02 11:11:05 -04:00
George Hartzell
63121a0c49 Add package for ack 
Add a package for [ack](http://beyondgrep.com/install/).  Simply install
the fatpacked script.

It uses '#!/usr/bin/env perl' and it very much not choosy about what
perl it needs.  For now just trust that there's one available, perhaps
someday we can/should uncomment the depends_on('perl').

Follows the methodolgy I used in nextflow.  Has the same
uninstall/install problem that nextflow has, there is an issue in
progress for that: https://github.com/LLNL/spack/issues/1308.

Tested on CentOS7.
 2016-08-02 11:11:05 -04:00
George Hartzell
12d1263980 Update several R packages (r-shiny prereqs) 
r-jsonlite 0.0.21 -> 1.0
r-mime     0.4    -> 0.5
rcpp       0.12.5 -> 0.12.6

CRAN is funny.  The older versions of these packages are still available
in package specific directories but the current version is not there, so
I don't see any way to make the older versions work.
 2016-08-02 11:10:41 -04:00
George Hartzell
6f332c7e4c Fix whitespace, make flake8 happ{y,ier}. 2016-08-02 11:10:12 -04:00
George Hartzell
bfcec69630 Add standard header, use spack helpers 
Added the standard header (stolen from R).

Touched up the install to use set_executable rather than doing it
myself.
 2016-08-02 11:10:12 -04:00
George Hartzell
4373a2b629 First cut package for nextflow, has issues 
This is my first cut at a package to support nextflow.  It's also my
first package.  It works, but has issues.  I'm going to submit a pull
request and get some coaching on how to deal with it.

One issue particular: if I install, then uninstall, then try to install
again (which uses the cached copy of the "distribution file"), it
explodes.
 2016-08-02 11:10:12 -04:00
Glenn Johnson
a57d94af03 Fix flake8 issues. 2016-08-02 09:53:57 -05:00
Denis Davydov
a1703bf70d kdiff3: add license block 2016-08-02 16:37:14 +02:00
Gilles Fourestey
dea7bbb4a0 added plumed 
* plumed : first version
* plumed : added dependencies and docs
 2016-08-02 15:06:46 +02:00
Denis Davydov
565bd5f51e atlas: revert to lapack 3.5.0 2016-08-02 13:52:32 +02:00
Denis Davydov
bef7e2645a atlas: flake8 fixes 2016-08-02 13:52:32 +02:00
Denis Davydov
f6a4a6b00f atlas: add install_test 2016-08-02 13:52:32 +02:00
Denis Davydov
0c0b37800d atlas: set (blas|lapack)_shared_lib 2016-08-02 13:52:32 +02:00