RPM package construction

Former-commit-id: b804704

INSTALL

@@ -47,3 +47,9 @@ sudo yum install libconfig libcurl gsl libxml2 zlib
 
 Install
 -------
+This step is not neccessary to run HPG Variant, but to install it in your system.
+
+In order to create RPM packages, you must install the rpmbuild tool by running the command 'sudo yum install rpm-build'.
+
+Type 'scons rpm' to create a file named 'hpg-variant_X.Y.fc17.x86_64.rpm' (with X.Y being the version number) in the subfolder 'rpm/rpmbuild/RPMS/x86_64'.
+Type 'sudo rpm -i hpg-variant_X.Y.fc17.x86_64.rpm', and don't forget to replace X.Y with the corresponding version number of your package.

SConstruct

@@ -46,11 +46,16 @@ env.Package(NAME           = 'hpg-variant',
             PACKAGEVERSION = 0,
             PACKAGETYPE    = 'src_targz',
             source         = env.FindSourceFiles() + env.FindHeaderFiles(progs) + 
-                             [ '#libs/libargtable2.a', '#libs/libcprops.a', 
+                             [ '#libs/libargtable2.a', '#libs/libcprops.a',
+                               Glob('#include/*.h'), Glob('#include/cprops/*.h'),
                                '#buildaux.py', '#buildvars.py', '#libs/common-libs/buildvars.py', '#libs/bioinfo-libs/buildvars.py',
+                               '#deb/SConscript', '#rpm/SConscript',
                                '#COPYING', '#INSTALL' ]
             )
 
 # Create Debian package
 if 'debian' in COMMAND_LINE_TARGETS:
     SConscript("deb/SConscript", exports = ['env'] )
+
+if 'rpm' in COMMAND_LINE_TARGETS:
+    SConscript("rpm/SConscript", exports = ['env'] )

deb/SConscript

@@ -21,8 +21,8 @@ DEBFILES = [
     ("usr/bin/hpg-var-gwas",                    "#bin/hpg-var-gwas"),
     ("usr/bin/hpg-var-vcf",                     "#bin/hpg-var-vcf"),
 
-    ("etc/hpg-variant/hpg-variant.conf",        "#bin/hpg-variant.cfg"),
-    ("etc/hpg-variant/vcf-info-fields.conf",    "#bin/vcf-info-fields.cfg"),
+    ("etc/hpg-variant/hpg-variant.conf",        "#bin/hpg-variant.conf"),
+    ("etc/hpg-variant/vcf-info-fields.conf",    "#bin/vcf-info-fields.conf"),
 
 ]
 

rpm/SConscript

@@ -0,0 +1,57 @@
+import hashlib, os, shutil, sys
+
+Import('env') # exported by parent SConstruct
+
+RPMNAME = "hpg-variant"
+RPMVERSION = "0.2"
+RPMARCH = "x86_64"
+RPMBUILDREQUIRES = "gcc,glibc-devel,scons,libconfig-devel,libcurl-devel,gsl-devel,libxml2-devel,zlib-devel".split(", ")
+RPMREQUIRES = "libconfig,libcurl,gsl,libxml2,zlib".split(", ") # what are we dependent on?
+RPMSUMMARY = "HPG Variant summary"
+RPMDESC = "HPG Variant retrieves the effect of genome mutations and allows to conduct analysis"
+RPMSECTION = "Application/Engineering"
+RPMSOURCE = "hpg-variant-0.2.tar.gz"
+RPMURL = "http://bioinfo.cipf.es"
+
+RPMBUILDIR = 'rpmbuild'
+RPMSPECFILE = "%s.spec" % RPMNAME
+
+
+# We want the package to be built when we build 'rpm'
+basename_rpmpkg = '%s-%s.fc17.%s.rpm' % (RPMNAME, RPMVERSION, RPMARCH)
+root_rpmpkg = "#" + basename_rpmpkg
+rpmpkg = os.path.join(RPMBUILDIR, 'RPMS', RPMARCH, basename_rpmpkg)
+env.Alias("rpm", rpmpkg)
+env.Depends(rpmpkg, RPMSPECFILE)
+env.Depends(root_rpmpkg, RPMSPECFILE)
+
+
+# 1) Create folder for building the packages
+if os.path.exists(RPMBUILDIR):
+    shutil.rmtree(RPMBUILDIR)
+
+SOURCES_DIR = os.path.join(RPMBUILDIR, 'SOURCES')
+SPECS_DIR = os.path.join(RPMBUILDIR, 'SPECS')
+
+os.mkdir(RPMBUILDIR)
+os.mkdir(os.path.join(RPMBUILDIR, 'BUILD'))
+os.mkdir(os.path.join(RPMBUILDIR, 'RPMS'))
+os.mkdir(SOURCES_DIR)
+os.mkdir(SPECS_DIR)
+os.mkdir(os.path.join(RPMBUILDIR, 'SRPMS'))
+
+# 2) Copy tarball to RPMBUILDIR/SOURCES subfolder
+shutil.copy('../%s' % RPMSOURCE, SOURCES_DIR)
+
+# 3) Copy .spec file to RPMBUILDIR folder
+shutil.copy(RPMSPECFILE, SPECS_DIR)
+
+# 4) Run rpmbuild with the .spec file as argument and copy to root folder
+SOURCETAR = os.path.join(SOURCES_DIR, RPMSOURCE)
+cmd = "rpmbuild --define='_topdir %s' -ba $SOURCE" % os.path.abspath(RPMBUILDIR)
+
+env.Command(rpmpkg, RPMSPECFILE, cmd)
+
+# 5) Copy to root folder
+#print "copy to %s" % root_rpmpkg
+#env.Command(root_rpmpkg, rpmpkg, Copy("$TARGET", "$SOURCE"))

rpm/hpg-variant.spec

@@ -0,0 +1,58 @@
+%define name hpg-variant
+%define version 0.2
+Name:           %{name}
+Version:        %{version}
+Release:        1%{?dist}
+Summary:        HPG Variant
+
+License:        GPLv2
+URL:            http://bioinfo.cipf.es
+Source0:        %{name}-%{version}.tar.gz
+
+BuildRequires:  gcc
+BuildRequires:  glibc-devel
+BuildRequires:  scons
+BuildRequires:  libconfig-devel
+BuildRequires:  libcurl-devel
+BuildRequires:  gsl-devel
+BuildRequires:  libxml2-devel
+BuildRequires:  zlib-devel
+
+Requires:       libconfig
+Requires:       libcurl
+Requires:       gsl
+Requires:       libxml2
+Requires:       zlib
+
+%description
+HPG Variant retrieves the effect of genome mutations and allows to conduct analysis
+
+%prep
+%setup -q
+
+
+%build
+scons
+
+
+%install
+rm -rf $RPM_BUILD_ROOT
+
+mkdir -p %{buildroot}%{_bindir}/
+cp bin/hpg-var-effect %{buildroot}%{_bindir}/
+cp bin/hpg-var-gwas   %{buildroot}%{_bindir}/
+cp bin/hpg-var-vcf    %{buildroot}%{_bindir}/
+
+mkdir -p %{buildroot}%{_sysconfdir}/%{name}/
+cp bin/hpg-variant.conf %{buildroot}%{_sysconfdir}/%{name}/
+cp bin/vcf-info-fields.conf %{buildroot}%{_sysconfdir}/%{name}/
+
+
+%files
+%doc
+%{_bindir}/*
+%{_sysconfdir}/*
+
+
+%changelog
+