added BLAST & NCBI-Toolkit

easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goalf-1.1.0-no-OFED.eb

@@ -0,0 +1,30 @@
+# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright (c) 2012 University of Luxembourg / Luxembourg Center for Systems Biomedicine
+# This work is part of HPCBIOS project:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+#
+# Author::    Fotis Georgatos <fotis.georgatos@uni.lu>
+# License::   MIT/GPL
+
+name = 'BLAST'
+version = '2.2.27'
+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': 'goalf', 'version': '1.1.0-no-OFED'}
+
+# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz
+sources = ['ncbi-blast-%s+-src.tar.gz' % version]
+source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%s/' % version]
+
+sanity_check_paths = {
+                      'files': ["bin/blastn", "bin/blastp", "bin/blastx"],
+                      'dirs': []
+                     }
+
+moduleclass = 'bio'

easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb

@@ -0,0 +1,32 @@
+# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright (c) 2012 University of Luxembourg / Luxembourg Center for Systems Biomedicine
+# This work is part of HPCBIOS project:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+#
+# Author::    Fotis Georgatos <fotis.georgatos@uni.lu>
+# License::   MIT/GPL
+
+name = 'NCBI-Toolkit'
+version = '9.0.0'
+
+homepage = 'http://www.ncbi.nlm.nih.gov/toolkit'
+description = """The NCBI Toolkit is a collection of utilities developed for the
+  production and distribution of GenBank, Entrez, BLAST, and related services
+  by the National Center for Biotechnology Information."""
+
+toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'}
+
+# eg. ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
+src_ver = '_'.join(version.split('.'))
+sources = ['ncbi_cxx--%s.tar.gz' % src_ver]
+source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/%s' % src_ver]
+
+patches = ['NCBI-Toolkit_make-install-fix.patch']
+
+sanity_check_paths = {
+                      'files': ["bin/blastn", "bin/blastp", "bin/blastx"],
+                      'dirs': []
+                     }
+
+moduleclass = 'bio'

easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit_make-install-fix.patch

@@ -0,0 +1,26 @@
+patch to fix make install issue, obtained from http://u14183.blogspot.be/2012/06/installing-ncbi-c-toolkit.html
+diff -ru ncbi_cxx--9_0_0.orig/src/build-system/Makefile.in.top ncbi_cxx--9_0_0/src/build-system/Makefile.in.top
+--- ncbi_cxx--9_0_0.orig/src/build-system/Makefile.in.top	2012-04-11 17:34:46.000000000 +0200
++++ ncbi_cxx--9_0_0/src/build-system/Makefile.in.top	2013-01-17 20:43:04.698601646 +0100
+@@ -39,7 +39,20 @@
+ 	-$(RMDIR) $(pincludedir)
+ 	$(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
+ 	$(INSTALL) $(lbindir)/* $(bindir)
+-	$(INSTALL) -m 644 $(llibdir)/* $(libdir)
++	cd $(llibdir) && \
++		for l in `find . -type f`; do $(INSTALL) -m 644 "$$l" $(libdir); done
++	mkdir $(libdir)/ncbi
++	mkdir $(libdir)/ncbi/mod
++	mkdir $(libdir)/schemas
++	mkdir $(libdir)/wmod
++	cd $(llibdir)/ncbi && \
++		for l in `find . -type f`; do $(INSTALL) -m 644 "$$l" $(libdir)/ncbi; done
++	cd $(llibdir)/ncbi/mod && \
++		for l in `find . -type f`; do $(INSTALL) -m 644 "$$l" $(libdir)/ncbi/mod; done
++	cd $(llibdir)/ncbi/schemas && \
++		for l in `find . -type f`; do $(INSTALL) -m 644 "$$l" $(libdir)/schemas; done
++	cd $(llibdir)/ncbi/wmod && \
++		for l in `find . -type f`; do $(INSTALL) -m 644 "$$l" $(libdir)/ncbi/wmod; done
+ 	-rm -f $(libdir)/lib*-static.a
+ 	cd $(libdir)  && \
+ 	    for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done