Fixed Clang 3.3

RELEASE_NOTES

@@ -1,10 +1,65 @@
 This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package.
 For more detailed information, please see the git log.
 
-The latest version of easybuild-easyconfig provides 1,340 easyconfig files, for 288 different software packages
-and 19 different compiler toolchains.
+The latest version of easybuild-easyconfig provides 1,631 easyconfig files, for 329 different software packages
+and 25 different (compiler) toolchains.
 
-v1.5.0.0 (May 31st 2013)
+v1.7.0.0 (September 2nd 2013)
+-----------------------------
+
+feature + bugfix release
+- added example easyconfig files for 15 new software packages:
+    - Glib (#294, #400), GLPK (#400), horton (#413), libint2 (#413), molmod (#413), Rosetta (#336), SCons (#336), Stacks (#367, #377), sympy (#413),
+      Qt (#294), XML-LibXML (#397), XML-Simple (#397), yaff (#413), YAML-Syck (#380), zsh (#376)
+- added additional easyconfigs for various software packages:
+    - BLAST, BamTools, BioPerl, Bison, Boost, bzip2, CMake, Cython, CUDA, FFTW, FIAT, GCC, GMP, gettext, git, h5py,
+      HDF5, libffi, libreadline, libxc, matplotlib, METIS, ncurses, Oases, Python, RAxML, ScientificPython, Szip,
+      tcsh, imkl, MVAPICH2, TotalView, VTune, WRF, zlib
+- added toolchain easyconfig files for HPCBIOS policies (#402, #407)
+    - HPCBIOS_BioInfo, HPCBIOS_Debuggers, HPCBIOS_LifeSciences, HPCBIOS_Math, HPCBIOS_Profilers
+- various enhancements, including:
+    - added more XML Perl modules to non-bare Perl easyconfigs (#375)
+- various 'bug' fixes, including:
+    - fix website/description in scipy easyconfigs (#399)
+    - specify OpenMPI libibverbs-dev(el) OS dependency in an OS-dependent way (#403)
+    - add patch file for M4 to fix building on systems with recent glibc (>=2.16) (#406)
+    - align moduleclass in R easyconfigs (#411)
+    - fixed filename of Biopython/CD-HIT easyconfig files (#407)
+    - disable parallel building of otcl (#419)
+
+v1.6.0.0 (July 11th 2013)
+-------------------------
+
+feature + bugfix release
+- added example easyconfig files for 26 new software packages:
+    - ALLPATHS-LG (#359), AutoMake (#347), BamTools (#319, #338), BLAT (#340), Biopython (#356), cairo (#361),
+      CCfits (#327), CD-HIT (#344), CFITSIO (#327), Diffutils (#347), FASTA (#358, #361), findutils (#347),
+      fontconfig (#361), gawk (#347), gettext (#361), GLIMMER (#357, #361), libidn (#361), LibTIFF (#347),
+      libungif (#347), make (#355), MUSCLE (#339), Oases (#354), pixman (#361), PLINK (#352), RCS (#347), SQLite (#347)
+- added additional easyconfigs for various software packages:
+    - ant, Bash, Bison, bzip2, cURL, expat, GCC, EasyBuild, freetype, FFTW, GDB, git, HMMER, JUnit, libreadline, libpng,
+      libtool, libxml2, libxslt, M4, makedepend, Mothur, MVAPICH2, Mercurial, ncurses, OpenBLAS, Python, ScaLAPACK, Tcl,
+      tcsh, TopHat, Trinity, Valgrind, Velvet, VTune, zlib
+      (see #169, #297, #298, #301, #309, #323, #331, #332, #341, #347, #349, #351, #355, #361)
+- various enhancements, including:
+    - added easyconfigs for ictce/5.4.0, ictce/5.5.0 and gmvolf/1.7.12 toolchain modules (#297, #332, #349)
+    - added a template sanity_check_paths as 'MUST' in TEMPLATE.eb (#329)
+    - introduced biodeps 'toolchain' to ease keeping common dependencies for bio* software in sync (#309)
+    - added collection of easyconfigs for ictce/5.3.0 (#309, #323)
+        - bam2fastq, bbFTP, BLAST, Boost, DL_POLY Classic, EMBOSS, FFTW, libharu, libxml2, libxslt, libyaml, lxml,
+          Mercurial, Mothur, mpi4py, ncurses, ns, orthomcl, otcl, PAML, Perl, PyYAML, pandas, problog, scikit-learn,
+          TiCCutils, TiMBL, TinySVM, TopHat, tclcl, YamCha
+    - added missing dependencies for various software packages (#323, #328, #348, #361)
+    - style fixes in various easyconfigs (#309, #323, #345, #349, #355, #361)
+- various 'bug' fixes, including:
+    - added 'pic' toolchain option for Perl goolf easyconfig (#299)
+    - fixed source URLs for R (use correct template 'version_major') (#302)
+    - synced libreadline easyconfigs w.r.t. ncurses dependency (#303)
+    - make sure EasyBuild configuration is initialized when running unit tests (#334)
+    - specify 'lowopt' (-O1) optimization level for OpenIFS, to avoid floating-point related issues (#328)
+    - fix naming of 'beagle-lib' (used to be 'BEAGLE'), to avoid name clashes with other software package(s) (#346)
+
+v1.5.0.0 (June 1st 2013)
 ------------------------
 
 feature + bugfix release

easybuild/easyconfigs/a/ACML/ACML-5.3.1-ifort-64bit.eb

@@ -10,3 +10,5 @@ computational fluid dynamics, financial analysis, oil and gas applications and m
 toolchain = {'name': 'dummy', 'version': 'dummy'}
 
 sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)]
+
+moduleclass = 'numlib'

easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-goalf-1.1.0-no-OFED.eb

@@ -20,9 +20,10 @@ sources = [
 patches = ['gmkpack_multi-lib.patch']
 
 dependencies = [
-                ('JasPer', '1.900.1'),
-                ('grib_api', '1.9.18'),
-                ('netCDF', '4.1.3'),  # can't use 4.2, because Fortran stuff is in seperate netCDF-Fortran install
-               ]
+    ('JasPer', '1.900.1'),
+    ('grib_api', '1.9.18'),
+    ('netCDF', '4.1.3'),  # can't use 4.2, because Fortran stuff is in seperate netCDF-Fortran install
+]
+builddependencies = [('Bison', '2.5')]
 
 moduleclass = 'geo'

easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-goolf-1.4.10.eb

@@ -20,9 +20,10 @@ sources = [
 patches = ['gmkpack_multi-lib.patch']
 
 dependencies = [
-                ('JasPer', '1.900.1'),
-                ('grib_api', '1.9.18'),
-                ('netCDF', '4.1.3'),  # can't use 4.2, because Fortran stuff is in seperate netCDF-Fortran install
-               ]
+    ('JasPer', '1.900.1'),
+    ('grib_api', '1.9.18'),
+    ('netCDF', '4.1.3'),  # can't use 4.2, because Fortran stuff is in seperate netCDF-Fortran install
+]
+builddependencies = [('Bison', '2.5')]
 
 moduleclass = 'geo'

easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-ictce-4.1.13.eb

@@ -23,9 +23,10 @@ patches = [
           ]
 
 dependencies = [
-                ('JasPer', '1.900.1'),
-                ('grib_api', '1.9.18'),
-                ('netCDF', '4.1.3'),
-               ]
+    ('JasPer', '1.900.1'),
+    ('grib_api', '1.9.18'),
+    ('netCDF', '4.1.3'),  # can't use 4.2, because Fortran stuff is in seperate netCDF-Fortran install
+]
+builddependencies = [('Bison', '2.5')]
 
 moduleclass = 'geo'

easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-ictce-5.3.0.eb

@@ -24,9 +24,10 @@ patches = [
           ]
 
 dependencies = [
-                ('JasPer', '1.900.1'),
-                ('grib_api', '1.9.18'),
-                ('netCDF', '4.1.3'),
-               ]
+    ('JasPer', '1.900.1'),
+    ('grib_api', '1.9.18'),
+    ('netCDF', '4.1.3'),  # can't use 4.2, because Fortran stuff is in seperate netCDF-Fortran install
+]
+builddependencies = [('Bison', '2.5')]
 
 moduleclass = 'geo'

easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb

@@ -0,0 +1,31 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 The Cyprus Institute
+# Authors::   Andreas Panteli <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>
+# License::   MIT/GPL
+#
+##
+
+name = 'ALLPATHS-LG'
+version = '46968'
+
+homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/'
+description = """ALLPATHS-LG, the new short read genome assembler."""
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+
+# source is moved over time, hence multiple URLs below
+source_urls = [
+    'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code',
+    'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06',
+    'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06',
+]
+sources = ['allpathslg-%(version)s.tar.gz']
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb

@@ -3,7 +3,7 @@ version = '1.9.0'
 
 homepage = 'http://ant.apache.org/'
 description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
-as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
 
 toolchain = {'name': 'dummy', 'version': ''}
 
@@ -22,3 +22,5 @@ sanity_check_paths = {
     'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
     'dirs': []
 }
+
+moduleclass = 'devel'

easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goalf-1.1.0-no-OFED.eb

@@ -28,9 +28,11 @@ swdir = version.rstrip(string.lowercase + string.uppercase)
 sources = [SOURCELOWER_TAR_GZ]
 source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % swdir, 'download']
 
+dependencies = [('bzip2', '1.0.6')]
+
 sanity_check_paths = {
-                      'files': ["bin/bfast"],
-                      'dirs': []
-                     }
+    'files': ["bin/bfast"],
+    'dirs': [],
+}
 
 moduleclass = 'bio'

easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb

@@ -28,9 +28,11 @@ swdir = version.rstrip(string.lowercase + string.uppercase)
 sources = [SOURCELOWER_TAR_GZ]
 source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % swdir, 'download']
 
+dependencies = [('bzip2', '1.0.6')]
+
 sanity_check_paths = {
-                      'files': ["bin/bfast"],
-                      'dirs': []
-                     }
+    'files': ["bin/bfast"],
+    'dirs': [],
+}
 
 moduleclass = 'bio'

easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-4.0.6.eb

@@ -28,9 +28,11 @@ swdir = version.rstrip(string.lowercase + string.uppercase)
 sources = [SOURCELOWER_TAR_GZ]
 source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % swdir, 'download']
 
+dependencies = [('bzip2', '1.0.6')]
+
 sanity_check_paths = {
-                      'files': ["bin/bfast"],
-                      'dirs': []
-                     }
+    'files': ["bin/bfast"],
+    'dirs': [],
+}
 
 moduleclass = 'bio'

easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb

@@ -28,9 +28,11 @@ swdir = version.rstrip(string.lowercase + string.uppercase)
 sources = [SOURCELOWER_TAR_GZ]
 source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % swdir, 'download']
 
+dependencies = [('bzip2', '1.0.6')]
+
 sanity_check_paths = {
-                      'files': ["bin/bfast"],
-                      'dirs': []
-                     }
+    'files': ["bin/bfast"],
+    'dirs': [],
+}
 
 moduleclass = 'bio'

easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-goolf-1.4.10-Python-2.7.3.eb

@@ -0,0 +1,41 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine
+# Authors::   Fotis Georgatos <fotis.georgatos@uni.lu>, Kenneth Hoste (UGent)
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+name = 'BLAST'
+version = '2.2.28'
+versionsuffix = '-Python-2.7.3'
+
+altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet.
+
+homepage = 'http://blast.ncbi.nlm.nih.gov/'
+description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
+ for comparing primary biological sequence information, such as the amino-acid
+ sequences of different proteins or the nucleotides of DNA sequences."""
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+
+# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz
+sources = ['ncbi-blast-%(version)s+-src.tar.gz']
+source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/']
+
+patches = ['%(name)s-%(version)s_ictce-fixes.patch']
+
+dependencies = [('Boost', '1.51.0', '-Python-2.7.3')]
+
+configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt'
+
+sanity_check_paths = {
+    'files': ["bin/blastn", "bin/blastp", "bin/blastx"],
+    'dirs': []
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-5.3.0-Python-2.7.3.eb

@@ -0,0 +1,41 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine
+# Authors::   Fotis Georgatos <fotis.georgatos@uni.lu>, Kenneth Hoste (UGent)
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+name = 'BLAST'
+version = '2.2.28'
+versionsuffix = '-Python-2.7.3'
+
+altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet.
+
+homepage = 'http://blast.ncbi.nlm.nih.gov/'
+description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
+ for comparing primary biological sequence information, such as the amino-acid
+ sequences of different proteins or the nucleotides of DNA sequences."""
+
+toolchain = {'name': 'ictce', 'version': '5.3.0'}
+
+# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz
+sources = ['ncbi-blast-%(version)s+-src.tar.gz']
+source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/']
+
+patches = ['%(name)s-%(version)s_ictce-fixes.patch']
+
+dependencies = [('Boost', '1.51.0', '-Python-2.7.3')]
+
+configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt'
+
+sanity_check_paths = {
+    'files': ["bin/blastn", "bin/blastp", "bin/blastx"],
+    'dirs': []
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-goolf-1.4.10.eb

@@ -11,7 +11,7 @@ name = 'BamTools'
 version = '2.2.3'
 
 homepage = 'https://github.com/pezmaster31/bamtools'
-description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files."
+description = """BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files."""
 
 toolchain = {'name': 'goolf', 'version': '1.4.10'}
 

easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-ictce-5.3.0.eb

@@ -0,0 +1,25 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 The Cyprus Institute
+# Authors::   Andreas Panteli <a.panteli@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>
+# License::   MIT/GPL
+#
+##
+
+name = 'BamTools'
+version = '2.2.3'
+
+homepage = 'https://github.com/pezmaster31/bamtools'
+description = """BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files."""
+
+toolchain = {'name': 'ictce', 'version': '5.3.0'}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = ['https://github.com/pezmaster31/bamtools/archive']
+
+builddependencies = [('CMake', '2.8.4')]
+
+files_to_copy = ["bin", "lib", "include", "docs", "LICENSE", "README"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb

@@ -21,11 +21,11 @@ description = """Bash is an sh-compatible command language interpreter that exec
 toolchain = {'name' : 'goalf', 'version' : '1.1.0-no-OFED'}
 
 sources = [SOURCELOWER_TAR_GZ]
-source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()]
+source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s']
 
 sanity_check_paths = {
-			'files': ["bin/bash"],
-			'dirs': []
-			}
+    'files': ["bin/bash"],
+    'dirs': []
+}
 
 moduleclass = 'tools'

easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb

@@ -21,11 +21,11 @@ description = """Bash is an sh-compatible command language interpreter that exec
 toolchain = {'name': 'goolf', 'version': '1.4.10'}
 
 sources = [SOURCELOWER_TAR_GZ]
-source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()]
+source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s']
 
 sanity_check_paths = {
-			'files': ["bin/bash"],
-			'dirs': []
-			}
+    'files': ["bin/bash"],
+    'dirs': []
+}
 
 moduleclass = 'tools'