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Author SHA1 Message Date
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
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
George Hartzell
d4274b32f2 Make flake8 happy (long lines) 2016-08-04 14:18:01 -04:00
Todd Gamblin
6ab78eb88e sbang filtering now works on non-writable files. (#1445) 
- sbang now changes mode to writable and restores mode if a file is not
  writable.
 2016-08-04 10:46:45 -07:00
Michael Kuhn
d7665a63e3 flake8 fixes 2016-08-04 19:04:48 +02:00
becker33
369b2ef01f Merge pull request #1330 from suraia/fix-ascii-graph 
Fix graph command with ASCII output
 2016-08-04 09:37:24 -07:00
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
bacfa91cfd Merge pull request #1444 from tobbez/fix_indent_spider 
Fix incorrect indentation in spack.util.web._spider
 2016-08-04 08:44:35 -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
Torbjörn Lönnemark
61b3ecb6d2 Fix flake8 issues 2016-08-04 16:28:14 +02:00
Denis Davydov
af8741c23c dealii: add optional python bindings 2016-08-04 16:11:14 +02:00
Torbjörn Lönnemark
a591e183bc Fix incorrect indentation 2016-08-04 16:09:49 +02:00
Michael Kuhn
584e5506f2 Update Score-P to 2.0 2016-08-04 14:24:25 +02:00
Michael Kuhn
2bd1a51193 flake8 fixes 2016-08-04 13:07:33 +02:00
Michael Kuhn
1578a95982 Fix tests. 2016-08-04 13:07:33 +02:00
Michael Kuhn
7affaca321 Fix graph command with ASCII output. 2016-08-04 13:07:33 +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
Todd Gamblin
be1158f7a3 Merge pull request #1433 from JRWynneIII/error_message_fix 
Fix typo for error message when compiler doesn't exist for arch
 2016-08-03 14:29:08 -07:00
James Riley Wynne III
f0609699ba Added parens to %'s arguments. Fixes #1432 2016-08-03 17:16:04 -04:00