Commit 9f977316 authored by Easy Build's avatar Easy Build

new file: a/ABAQUS/ABAQUS-2017-hotfix-1721.eb

	new file:   a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb
	new file:   a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb
	new file:   a/AMOS/AMOS-3.1.0_GCC-4.7.patch
	new file:   a/ARB/ARB-5.5-goolf-1.4.10.eb
	new file:   a/ARB/ARB-5.5_xflags.patch
	new file:   a/ARB/ARB-5.5_xmkmf.patch
	modified:   duplicate
	modified:   it4i
	new file:   remove_list
	modified:   test.sh
	deleted:    .test.sh.swp
parent 9d8e0579
name = 'ABAQUS'
version = '2017'
hotfix = '1721'
versionsuffix = '-hotfix-%s' % hotfix
homepage = 'http://www.simulia.com/products/abaqus_fea.html'
description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit
dynamics FEA."""
toolchain = {'name': 'dummy', 'version': ''}
sources = [
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.6-6.tar',
# hotfixes
'%%(version)s.FP.CFA.%s.Part_3DEXP_SimulationServices.Linux64.tar' % hotfix,
'%%(version)s.FP.CFA.%s.Part_SIMULIA_Abaqus_CAE.Linux64.tar' % hotfix,
]
moduleclass = 'cae'
##
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
# 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
##
easyblock = 'ConfigureMake'
name = 'AMOS'
version = '3.1.0'
homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS'
description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
toolchain = {'name': 'goolf', 'version': '1.4.10'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_GZ]
source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')]
patches = ['AMOS-3.1.0_GCC-4.7.patch']
dependencies = [
('expat', '2.1.0'),
('MUMmer', '3.23'),
]
sanity_check_paths = {
'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'],
'dirs': []
}
parallel = 1 # make crashes otherwise
moduleclass = 'bio'
##
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
# 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
##
easyblock = 'ConfigureMake'
name = 'AMOS'
version = '3.1.0'
homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS'
description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
toolchain = {'name': 'ictce', 'version': '5.3.0'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_GZ]
source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')]
dependencies = [
('expat', '2.1.0'),
('MUMmer', '3.23'),
]
sanity_check_paths = {
'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'],
'dirs': []
}
parallel = 1 # make crashes otherwise
moduleclass = 'bio'
diff -ru amos-3.1.0.orig/src/Align/find-tandem.cc amos-3.1.0/src/Align/find-tandem.cc
--- amos-3.1.0.orig/src/Align/find-tandem.cc 2011-07-25 01:27:26.000000000 +0200
+++ amos-3.1.0/src/Align/find-tandem.cc 2013-03-27 13:51:23.024914923 +0100
@@ -7,6 +7,7 @@
#include <vector>
#include <ctime>
#include <sys/time.h>
+#include <unistd.h>
using namespace std;
const int OFFSET_TABLE_SIZE = 100;
name = 'ARB'
version = '5.5'
homepage = 'http://www.arb-home.de/'
description = """The ARB software is a graphically oriented package comprising various tools for sequence database
handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked
to the respective sequence entries is structured according to phylogeny or other user defined criteria."""
toolchain = {'name': 'goolf', 'version': '1.4.10'}
# download from http://download.arb-home.de/release/arb_5.5, and rename to include version
sources = ['%(namelower)s-%(version)s-src.tgz']
patches = [
'%(name)s-%(version)s_xmkmf.patch',
'%(name)s-%(version)s_xflags.patch',
]
dependencies = [
('libpng', '1.6.6'),
('LibTIFF', '4.0.3'),
('Java', '1.7.0_15', '', True),
('lynx', '2.8.7'),
('makedepend', '1.0.4'),
('imake', '1.0.5'),
('libXt', '1.1.4'),
('motif', '2.3.4'), # libXm
('libXpm', '3.5.11'),
('libXaw', '1.0.12'),
('Perl', '5.16.3'),
('libxslt', '1.1.28'),
('freeglut', '2.8.1'),
('Sablotron', '1.0.3'),
('libxml2', '2.9.1'),
]
moduleclass = 'bio'
--- Makefile.orig 2013-09-26 16:43:53.016909280 +0200
+++ Makefile 2013-09-26 16:48:39.953144714 +0200
@@ -31,7 +31,7 @@
# configurable in config.makefile
#
# -----------------------------------------------------
-# Read configuration
+# Read configuration
include config.makefile
ifeq ($(LD_LIBRARY_PATH),'')
@@ -121,10 +121,10 @@
# Enable several warnings
extended_warnings := -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
- extended_cpp_warnings := -Wnon-virtual-dtor -Wreorder -Wpointer-arith
+ extended_cpp_warnings := -Wnon-virtual-dtor -Wreorder -Wpointer-arith
ifneq ('$(USING_GCC_3XX)','')
extended_cpp_warnings += -Wdisabled-optimization -Wmissing-format-attribute
- extended_cpp_warnings += -Wmissing-noreturn # -Wfloat-equal
+ extended_cpp_warnings += -Wmissing-noreturn # -Wfloat-equal
endif
ifneq ('$(USING_GCC_4XX)','')
# extended_cpp_warnings += -Wwhatever
@@ -135,7 +135,7 @@
endif
endif
-#---------------------- developer
+#---------------------- developer
ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
ifdef dflags
@@ -153,7 +153,7 @@
endif
ifeq ($(ARB_64),1)
- dflags += -DARB_64 #-fPIC
+ dflags += -DARB_64 #-fPIC
lflags +=
shared_cflags += -fPIC
@@ -175,7 +175,7 @@
# build 32-bit ARB version on 64-bit host
CROSS_LIB:=# empty = autodetect below
cflags += -m32
- lflags += -m32 -m elf_i386
+ lflags += -m32 -m elf_i386
else
# build 32-bit ARB version on 32-bit host
CROSS_LIB:=/lib
@@ -214,20 +214,20 @@
XHOME:=/usr/X11R6
endif
-XINCLUDES:=-I$(XHOME)/include
+XINCLUDES:=$(CPPFLAGS)
ifdef DARWIN
XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
- XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
+ XLIBS := -$(LDFLAGS) L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
else
- XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
+ XLIBS:=$(LDFLAGS) -L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
endif
#---------------------- open GL
-ifeq ($(OPENGL),1)
+ifeq ($(OPENGL),1)
cflags += -DARB_OPENGL # activate OPENGL code
GL := gl # this is the name of the OPENGL base target
GL_LIB := -lGL -L$(ARBHOME)/GL/glAW -lglAW
@@ -280,7 +280,7 @@
endif
endif
-# -------------------------------------------------------------------------
+# -------------------------------------------------------------------------
# Don't put any machine/version/etc conditionals below!
# (instead define variables above)
# -------------------------------------------------------------------------
@@ -335,9 +335,9 @@
lflags:=
-# -------------------------
-# Main arb targets:
-# -------------------------
+# -------------------------
+# Main arb targets:
+# -------------------------
first_target:
$(MAKE) checks
@@ -521,7 +521,7 @@
# ---------------------
-check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
+check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
@echo Your setup seems to be ok.
checks: check_setup check_tabs
@@ -558,7 +558,7 @@
cflags:=$(cflags) -DFAKE_VTAB_PTR=char
endif
-# -------------------------------
+# -------------------------------
# old PTSERVER or PTPAN?
ifeq ($(PTPAN),1)
@@ -583,7 +583,7 @@
ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
endif
-# -------------------------------
+# -------------------------------
# List of all Directories
ARCHS = \
@@ -894,7 +894,7 @@
$(ARCHS_PROBE_COMMON) \
$(ARCHS_PT_SERVER) \
-$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) shared_libs
+$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) shared_libs
@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) || ( \
echo Link $@ ; \
echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)" ; \
@@ -1008,7 +1008,7 @@
NAMES_COM/server.dummy : comtools
NAMES_COM/client.dummy : comtools
-com_probe: PROBE_COM/PROBE_COM.dummy
+com_probe: PROBE_COM/PROBE_COM.dummy
com_names: NAMES_COM/NAMES_COM.dummy
com_all: com_probe com_names
@@ -1151,7 +1151,7 @@
#********************************************************************************
depends:
- $(MAKE) comtools
+ $(MAKE) comtools
@echo "$(SEP) Partially build com interface"
$(MAKE) PROBE_COM/PROBE_COM.depends
$(MAKE) NAMES_COM/NAMES_COM.depends
@@ -1162,10 +1162,10 @@
depend: depends
proto_tools:
- @echo $(SEP) Building prototyper
+ @echo $(SEP) Building prototyper
$(MAKE) AISC_MKPTPS/AISC_MKPTPS.dummy
-#proto: proto_tools TOOLS/TOOLS.dummy
+#proto: proto_tools TOOLS/TOOLS.dummy
proto: proto_tools
@echo $(SEP) Updating prototypes
$(MAKE) \
@@ -1270,7 +1270,7 @@
all
@$(MAKE) testperlscripts
-testperlscripts:
+testperlscripts:
@$(MAKE) -C PERL_SCRIPTS/test test
perl_clean:
@@ -1346,16 +1346,16 @@
$(MAKE) all
tarfile: rebuild
- $(MAKE) addlibs
+ $(MAKE) addlibs
util/arb_compress
tarfile_quick: all
- $(MAKE) addlibs
+ $(MAKE) addlibs
util/arb_compress
-save: sourcetarfile
+save: sourcetarfile
-# test early whether save will work
+# test early whether save will work
testsave:
@util/arb_srclst.pl >/dev/null
@@ -1377,14 +1377,14 @@
touch SOURCE_TOOLS/inc_major.stamp
$(MAKE) do_release
-do_release:
+do_release:
@echo Building release
@echo PATH=$(PATH)
@echo ARBHOME=$(ARBHOME)
-rm arb.tgz arbsrc.tgz
$(MAKE) testsave
$(MAKE) templ # auto upgrades version early
- $(MAKE) tarfile
+ $(MAKE) tarfile
$(MAKE) sourcetarfile
release_quick:
@@ -1407,7 +1407,7 @@
arbapplications: nt pa ed e4 wetc pt na nal di ph ds pgt
# optionally things (no real harm for ARB if any of them fails):
-arbxtras: tg pst a3 xmlin
+arbxtras: tg pst a3 xmlin
tryxtras:
@echo $(SEP)
--- Makefile.orig 2013-07-16 14:55:29.971221036 +0200
+++ Makefile 2013-07-16 14:58:28.543495360 +0200
@@ -68,7 +68,7 @@
4.3.1 4.3.2 4.3.3 \
4.4.1 4.4.3 \
4.6.1 \
- 4.7.1
+ 4.7.1 4.7.2
ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
@@ -322,7 +322,7 @@
ifdef DARWIN
XMKMF := $(PREFIX)/bin/xmkmf
else
- XMKMF := /usr/bin/X11/xmkmf
+ XMKMF := xmkmf
endif
MAKEDEPEND_PLAIN = makedepend
......@@ -2,3 +2,17 @@ a47f78ce229d82b7818feb0d9e2e9480
a47f78ce229d82b7818feb0d9e2e9480
37a67325bd697ba16456d47f96a809e9
a47f78ce229d82b7818feb0d9e2e9480;CUDA-7.5.18.eb
42c0a56911761bebefa424a6580e80fe;ARB-5.5-goolf-1.4.10.eb
a47f78ce229d82b7818feb0d9e2e9480;CUDA-7.5.18.eb
1af592f5c53593710e9a65d4aecaa8f6;ABAQUS-2017-hotfix-1721.eb
4f649bd51dadf7c43d0b5118db54d915;AMOS-3.1.0-goolf-1.4.10.eb
e8b947919b8aeb4a6a394d6831f5d6a4;AMOS-3.1.0-ictce-5.3.0.eb
42c0a56911761bebefa424a6580e80fe;ARB-5.5-goolf-1.4.10.eb
a47f78ce229d82b7818feb0d9e2e9480;CUDA-7.5.18.eb
37a67325bd697ba16456d47f96a809e9;GSL-2.3-intel-2017a.eb
22df523f7cc85cc59ef94b864ba42cb8;HPL-2.2-intel-2017b.eb
454e580a5ededc4fc3ef984aac28bfe9;Mesa-12.0.2-intel-2016b.eb
d5a4360bcafc8486b843c83767044a7d;ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb
0515e2cba0b6b96e9a955ad98a991119;SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb
11f2dc760748e6e004378c8e2b277b70;XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb
515233dc386f6b025bc6c88ec8377c65;xcb-proto-1.11.eb
......@@ -47,6 +47,7 @@ f0e89dff152696e2faa04d68dcb1f2e0;arpack-ng-3.1.5-ictce-7.1.2.eb
313521c944c200d1700d40c67bd74239;ABAQUS-6.12.1-linux-x86_64.eb
9555dee6a3fdc68138b839751509fc68;ABAQUS-6.13.5-linux-x86_64.eb
32f763ef588dd67a21c395fcc86806db;ABAQUS-6.14.1-linux-x86_64.eb
1af592f5c53593710e9a65d4aecaa8f6;ABAQUS-2017-hotfix-1721.eb
eda68e7a1bb264ea688d43f49f433912;ADF-2014.02.eb
f560888282eae76d57e7a1c1c8ed7a02;ADF-2014.11.r48287-intel-2016a.eb
a3aa2fe5a990af4fc1ec579118692d0f;ADF-2016.101.eb
......@@ -65,6 +66,9 @@ e5f7b80ace520a57a48799e1b758cbfb;Amber-16-iomkl-2016.07-AmberTools-16-patchlevel
9b4a3bdd94004db98200fe603075a9df;angsd-0.910-foss-2016a.eb
aaaa90e3d19473c1e1c80e58bf608f03;ATK-2.20.0.eb
27099b4bb553a10ec286fb5a08e1d48e;astroid-1.5.3-Python-2.7.13-base.eb
42c0a56911761bebefa424a6580e80fe;ARB-5.5-goolf-1.4.10.eb
4f649bd51dadf7c43d0b5118db54d915;AMOS-3.1.0-goolf-1.4.10.eb
e8b947919b8aeb4a6a394d6831f5d6a4;AMOS-3.1.0-ictce-5.3.0.eb
1ae55bc8022a90c788a2e0471f55cd4a;BCFtools-1.3-foss-2015g.eb
9ea3e0c9fb112aebb83fe707fe14c57d;BCFtools-1.2-foss-2015a.eb
d6b84288361d110b6be170792281811d;BCFtools-1.2-intel-2015a.eb
......
0515e2cba0b6b96e9a955ad98a991119;SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb
11f2dc760748e6e004378c8e2b277b70;XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb
1af592f5c53593710e9a65d4aecaa8f6;ABAQUS-2017-hotfix-1721.eb
22df523f7cc85cc59ef94b864ba42cb8;HPL-2.2-intel-2017b.eb
37a67325bd697ba16456d47f96a809e9;GSL-2.3-intel-2017a.eb
42c0a56911761bebefa424a6580e80fe;ARB-5.5-goolf-1.4.10.eb
454e580a5ededc4fc3ef984aac28bfe9;Mesa-12.0.2-intel-2016b.eb
4f649bd51dadf7c43d0b5118db54d915;AMOS-3.1.0-goolf-1.4.10.eb
515233dc386f6b025bc6c88ec8377c65;xcb-proto-1.11.eb
a47f78ce229d82b7818feb0d9e2e9480;CUDA-7.5.18.eb
d5a4360bcafc8486b843c83767044a7d;ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb
e8b947919b8aeb4a6a394d6831f5d6a4;AMOS-3.1.0-ictce-5.3.0.eb
......@@ -3,7 +3,15 @@
printf "\033c"
DIR=`pwd`
format="| MD5 | %-32s | Name | %-80s | \n"
red=$'\e[1;31m'
grn=$'\e[1;32m'
yel=$'\e[1;33m'
blu=$'\e[1;34m'
mag=$'\e[1;35m'
cyn=$'\e[1;36m'
end=$'\e[0m'
format="| MD5 | %-32s | Name | %-80s\n"
echo -n " Preparing IT4I .......... ["
for a in `find /apps/easybuild/easyconfigs-develop/easybuild/easyconfigs/ -type f -name *.eb`; do md5sum $a | grep -v "__archive__" | sed 's| .||' | cut -d '/' -f 1,8 | tr "/" ";" | sed 's|apps||'; done > develop && echo -e "\e[32m OK \e[0m]" || echo -e "\e[31mFAIL\e[0m]"
......@@ -11,6 +19,8 @@ for a in `find /apps/easybuild/easyconfigs-develop/easybuild/easyconfigs/ -type
echo -n " Preparing develop ....... ["
for a in `find . -type f -name *.eb`; do md5sum $a | grep -v "__archive__" | sed 's| .||' | cut -d '/' -f 1,4 | tr "/" ";" | sed 's|apps||'; done > it4i && echo -e "\e[32m OK \e[0m]" || echo -e "\e[31mFAIL\e[0m]"
echo ""
for x in `cat develop`; do
X=$(echo $x | cut -d ';' -f 1)
Xname=$(echo $x | cut -d ';' -f 2)
......@@ -21,5 +31,10 @@ for x in `cat develop`; do
break
fi
done
printf "$format" "$X" "$Xname"
printf "$format" "${grn}$X${end}" "${grn}$Xname${end}"
done
echo ""
for read in `cat duplicate`; do grep "$read" it4i; done | sort -u > remove_list
rm duplicate it4i develop
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