diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goalf-1.1.0-no-OFED.eb new file mode 100644 index 000000000000..89c19fd2e916 --- /dev/null +++ b/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 +# 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' diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb new file mode 100644 index 000000000000..8f04a3cf9eae --- /dev/null +++ b/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 +# 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' diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit_make-install-fix.patch b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit_make-install-fix.patch new file mode 100644 index 000000000000..29a7e5867223 --- /dev/null +++ b/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