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dpo / jellyfish.rb
Created February 17, 2014 19:44
require 'formula'
class Jellyfish < Formula
homepage 'http://www.cbcb.umd.edu/software/jellyfish/'
url 'ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.0.0.tar.gz'
sha1 '65985a197e1fe57fd3965c055616eaafe0a748e8'
fails_with :clang do
cause 'gcc >= 4.4 is required to compile Jellyfish.'
end
@dpo
dpo / bedops.rb
Created February 18, 2014 20:56
require 'formula'
class Bedops < Formula
homepage 'https://github.com/bedops/bedops'
url 'https://github.com/bedops/bedops/archive/v2.4.1-rc1.tar.gz'
sha1 '436c769af8ffac70f4d7f02922915d3c71c5af88'
head 'https://github.com/bedops/bedops.git'
fails_with :clang
fails_with :llvm
@dpo
dpo / a.rb
Created February 20, 2014 19:03
[dpo@Aragorn:test ]$ ./hs071_c
******************************************************************************
This program contains Ipopt, a library for large-scale nonlinear optimization.
Ipopt is released as open source code under the Eclipse Public License (EPL).
For more information visit http://projects.coin-or.org/Ipopt
******************************************************************************
This is Ipopt version 3.11.7, running with linear solver mumps.
NOTE: Other linear solvers might be more efficient (see Ipopt documentation).
@dpo
dpo / ipopt.rb
Created February 20, 2014 19:38
require 'formula'
class Ipopt < Formula
homepage 'https://projects.coin-or.org/Ipopt'
url 'http://www.coin-or.org/download/source/Ipopt/Ipopt-3.11.7.tgz'
sha1 '4547db1acbd65aad9edbed115a7812fbfd6d2d3a'
head 'https://projects.coin-or.org/svn/Ipopt/trunk', :using => :svn
option 'without-check', 'Skip build-time tests (not recommended)'
@dpo
dpo / velvet.rb
Created February 22, 2014 17:44
require 'formula'
class Velvet < Formula
homepage 'http://www.ebi.ac.uk/~zerbino/velvet/'
url 'http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz'
sha1 '216f0941609abf3a73adbba19ef1f364df489d18'
head 'https://github.com/dzerbino/velvet.git'
option 'with-maxkmerlength=<value>', 'Specify max kmer length'
@dpo
dpo / a.rb
Created February 28, 2014 02:58
diff --git a/complex16/second.F b/complex16/second.F
index 77fb342..cf0acbd 100644
--- a/complex16/second.F
+++ b/complex16/second.F
@@ -23,10 +23,10 @@
#ifdef _AIX
REAL ETIME_
- EXTERNAL ETIME_
+C EXTERNAL ETIME_
@dpo
dpo / propack.diff
Created February 28, 2014 19:32
diff --git a/complex16/Examples/Makefile b/complex16/Examples/Makefile
index 900f2b6..d343e78 100644
--- a/complex16/Examples/Makefile
+++ b/complex16/Examples/Makefile
@@ -45,15 +45,15 @@ compare.$(PLAT).x: lib compare.o
test:
@( echo "==Testing DOUBLE COMPLEX version without implicit restart.=="; \
- example.$(PLAT).x < example.in; \
+ ./example.$(PLAT).x < example.in; \
@dpo
dpo / r.rb
Created March 8, 2014 08:06
require 'formula'
class R < Formula
homepage 'http://www.r-project.org'
url 'http://cran.r-project.org/src/base/R-3/R-3.0.3.tar.gz'
sha1 '82e83415d27a2fbbdcacb41c4aa14d8b36fdf470'
head 'https://svn.r-project.org/R/trunk'
option 'without-check', 'Skip build-time tests (not recommended)'
@dpo
dpo / run_latex_build.py
Created March 11, 2014 14:59
Sublime Text Multi-Build System: Run Several Build Systems in Sequence and Reset to Last One
import sublime_plugin
class RunLatexBuildCommand(sublime_plugin.WindowCommand):
def run(self, build_systems=None):
if build_systems is None:
return
reset_to = build_systems[-1]
@dpo
dpo / 02.make
Created April 7, 2014 01:54
This file has been truncated, but you can view the full file.
/usr/local/Cellar/cmake/2.8.12.2/bin/cmake -H/tmp/trilinos-YaYf/trilinos-11.6.1-Source -B/tmp/trilinos-YaYf/trilinos-11.6.1-Source/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/Cellar/cmake/2.8.12.2/bin/cmake -E cmake_progress_start /tmp/trilinos-YaYf/trilinos-11.6.1-Source/build/CMakeFiles /tmp/trilinos-YaYf/trilinos-11.6.1-Source/build/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
/usr/bin/make -f cmake/tribits/package_arch/UnitTests/CTestScriptsUnitTests/CMakeFiles/TrilinosFramework_GenericDriver.dir/build.make cmake/tribits/package_arch/UnitTests/CTestScriptsUnitTests/CMakeFiles/TrilinosFramework_GenericDriver.dir/depend
/usr/bin/make -f packages/teuchos/core/src/CMakeFiles/teuchoscore.dir/build.make packages/teuchos/core/src/CMakeFiles/teuchoscore.dir/depend
/usr/bin/make -f packages/teuchos/parameterlist/test/ParameterList/CMakeFiles/TeuchosParameterList_ParameterListFileCopies.dir/build.make packages/teuchos/parameterlist/test/ParameterList/CMakeFiles/TeuchosPa