add easyconfigs for pplacer and OCaml deps (REVIEW)

easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb

@@ -6,36 +6,43 @@
 # License::   MIT/GPL
 # $Id$
 ##
-
-easyblock = 'ConfigureMake'
-
-name = "OCaml"
-version = "4.01.0"
+name = 'OCaml'
+version = '4.01.0'
 
 homepage = 'http://ocaml.org/'
 description = """OCaml is a general purpose industrial-strength programming language
  with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria
  it benefits from one of the most advanced type systems and supports functional,
  imperative and object-oriented styles of programming."""
 
-toolchain = {'version': '1.4.10', 'name': 'goolf'}
-
-sources = [SOURCELOWER_TAR_GZ]
-sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1])
-source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir]
-
-builddependencies = [('Autoconf', '2.69')]
-dependencies = [('ncurses', '5.9')]
-
-prefix_opt = "-prefix "
-buildopts = "world.opt"
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+
+opam_ver = '1.2.2'
+source_urls = [
+    'http://caml.inria.fr/pub/distrib/ocaml-%s' % '.'.join(version.split('.')[:2]),
+    'https://github.com/ocaml/opam/releases/download/%s' % opam_ver,
+]
+sources = [
+    'ocaml-%(version)s.tar.gz',
+    'opam-full-%s.tar.gz' % opam_ver,
+]
+
+builddependencies = [('Autotools', '20150215', '', ('GCC', '4.7.2'))]
+dependencies = [
+    ('ncurses', '5.9'),
+    ('libreadline', '6.3'),
+    ('GSL', '1.16'),
+]
 
 # parallel build tends to break
 parallel = 1
 
-sanity_check_paths = {
-    'files': ["bin/ocaml", "bin/ocamlc"],
-    'dirs': []
-}
+# handled by OPAM, order matters!
+exts_list = [
+    ('ocamlfind', '1.5.5'),
+    ('batteries', '2.3.1'),
+    ('ocaml+twt', '0.94.0'),
+    ('gsl', '1.18.5'),
+]
 
 moduleclass = 'lang'

easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb

@@ -0,0 +1,50 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+##
+name = 'OCaml'
+version = '4.01.0'
+
+homepage = 'http://ocaml.org/'
+description = """OCaml is a general purpose industrial-strength programming language
+ with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria
+ it benefits from one of the most advanced type systems and supports functional,
+ imperative and object-oriented styles of programming."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+opam_ver = '1.2.2'
+source_urls = [
+    'http://caml.inria.fr/pub/distrib/ocaml-%s' % '.'.join(version.split('.')[:2]),
+    'https://github.com/ocaml/opam/releases/download/%s' % opam_ver,
+]
+sources = [
+    'ocaml-%(version)s.tar.gz',
+    'opam-full-%s.tar.gz' % opam_ver,
+]
+
+patches = ['OCaml-%(version)s_icc-fixes.patch']
+
+builddependencies = [('Autotools', '20150215')]
+dependencies = [
+    ('ncurses', '5.9'),
+    ('libreadline', '6.2'),
+    ('GSL', '1.16'),
+]
+
+# parallel build tends to break
+parallel = 1
+
+# handled by OPAM, order matters!
+exts_list = [
+    ('ocamlfind', '1.5.5'),
+    ('batteries', '2.3.1'),
+    ('ocaml+twt', '0.94.0'),
+    ('gsl', '1.18.5'),
+]
+
+moduleclass = 'lang'

easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch

@@ -0,0 +1,22 @@
+fix for Fatal error: exception Invalid_argument("gettimeofday not implemented")
+author: Kenneth Hoste (HPC-UGent)
+--- configure.orig	2015-10-06 10:19:12.763826416 +0200
++++ configure	2015-10-06 10:19:56.005026703 +0200
+@@ -1015,7 +1015,7 @@
+ fi
+
+ has_select=no
+-if sh ./hasgot select && \
++if cc="$cc -wd165" sh ./hasgot select && \
+    sh ./hasgot -i sys/types.h $select_include -t fd_set ; then
+   echo "select() found."
+   echo "#define HAS_SELECT" >> s.h
+@@ -1084,7 +1084,7 @@
+ fi
+
+ has_gettimeofday=no
+-if sh ./hasgot gettimeofday; then
++if cc="$cc -wd165" sh ./hasgot gettimeofday; then
+   echo "gettimeofday() found."
+   echo "#define HAS_GETTIMEOFDAY" >> s.h
+   has_gettimeofday="yes"

easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb

@@ -17,10 +17,9 @@ description = """OCaml is a general purpose industrial-strength programming lang
 
 toolchain = {'name': 'foss', 'version': '2015a'}
 
-ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1])
 opam_ver = '1.2.2'
 source_urls = [
-    'http://caml.inria.fr/pub/distrib/%s' % ocaml_sourcedir,
+    'http://caml.inria.fr/pub/distrib/ocaml-%s' % '.'.join(version.split('.')[:2]),
     'https://github.com/ocaml/opam/releases/download/%s' % opam_ver,
 ]
 sources = [

easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb

@@ -0,0 +1,56 @@
+easyblock = 'MakeCp'
+
+name = 'pplacer'
+version = '1.1.alpha16'
+
+homepage = 'http://matsen.fhcrc.org/pplacer/'
+description = """Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic
+ likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give
+ useful information about uncertainty, and to offer advanced visualization and downstream analysis."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+source_urls = [
+    'https://github.com/matsen/pplacer/archive/',
+    'https://github.com/matsen/pplacer-opam-repository/archive/',
+]
+sources = [
+    'v%(version)s.tar.gz',
+    'ba5e766.tar.gz',  # pplacer-opam-repository (20151002)
+]
+
+patches = ['pplacer-%(version)s_fix-sqlite3-req-pkg.patch']
+
+ocaml = 'OCaml'
+ocamlver = '4.01.0'
+versionsuffix = '-%s-%s' % (ocaml, ocamlver)
+dependencies = [
+    (ocaml, ocamlver),
+    ('zlib', '1.2.7'),  # for CamlZIP OCaml package
+    ('GSL', '1.16'),  # for GSL-OCaml package
+    ('SQLite', '3.8.6'),  # for SQLite3-OCaml package
+]
+builddependencies = [
+    ('M4', '1.4.17'),
+]
+
+# see http://matsen.github.io/pplacer/compiling.html#opam
+prebuildopts = "rm -rf %(installdir)s && export OPAMROOT=%(installdir)s && opam init && "
+prebuildopts += "opam repo add pplacer-deps %(builddir)s/pplacer-opam-repository*/ && "
+prebuildopts += "opam update pplacer-deps && eval `opam config env` && "
+prebuildopts += "export OCAML_BACKEND=gcc && cat opam-requirements.txt | xargs opam install -y && "
+prebuildopts += "echo 'let version = \"v%(version)s\"\n' > common_src/version.ml && "
+
+# parallel build tends to break
+parallel = 1
+
+files_to_copy = ['bin']
+
+sanity_check_paths = {
+    'files': ['bin/guppy', 'bin/pplacer', 'bin/rppr'],
+    'dirs': [],
+}
+
+sanity_check_commands = [('pplacer', '--version | grep %(version)s')]
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16_fix-sqlite3-req-pkg.patch

@@ -0,0 +1,11 @@
+fix name of required sqlite3-ocaml package
+see also https://github.com/matsen/pplacer/commit/4ae1c6803486a6460a776b6807657a3bcc4005da
+--- opam-requirements.txt.orig	2015-10-06 16:38:42.246475661 +0200
++++ opam-requirements.txt	2015-10-06 16:38:50.586708932 +0200
+@@ -4,5 +4,5 @@
+ mcl.12-068oasis3
+ batteries.2.1.0
+ ocaml-gsl.0.6.3
+-sqlite3-ocaml.1.6.3
++sqlite3.1.6.3
+ camlzip.1.05