Package for bcl2fastq2 (updates libxslt) (#4234)

* Add v1.1.26 and make crypto a variant

I need 1.1.26 for bcl2fastq2.

I also need to build it without crypto support.

* Initial support for bcl2fastq2

* Clean up commentary, messages, names

No substantial changes intended, just cleanup.

* fix flake8 and extra import

* The masked grammarian strikes again...

* Be normal (messages don't end in periods)

* When +crypto, add --with-crypto

Add `--with-crypto` to configure args when user hasn't explicitly set
`~crypto`.

* self.spec.satisfies is unsatisfying, in is in instead

See #4135, self.spec.satisfies has issues.  @adamjstewart suggests
simply using in.

4 files changed, 131 insertions, 2 deletions

diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/cmake-macros.patch b/var/spack/repos/builtin/packages/bcl2fastq2/cmake-macros.patch
new file mode 100644
index 0000000000..a799ef68e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bcl2fastq2/cmake-macros.patch
@@ -0,0 +1,10 @@
+--- a/src/cmake/bcl2fastq_redist_macros.cmake        2017-05-11 15:03:27.652495488 -0700
++++ b/src/cmake/bcl2fastq_redist_macros.cmake        2017-05-11 15:06:38.326745889 -0700
+@@ -30,6 +30,7 @@
+        message(" Found: ${libname}, correct version ${version}")
+        message("   ${${libname}_UPPER}_INCLUDE_DIR = ${${${libname}_UPPER}_INCLUDE_DIR}")
+        message("   ${${libname}_UPPER}_LIBRARIES = ${${${libname}_UPPER}_LIBRARIES}")
++       set (HAVE_${${libname}_UPPER} true CACHE BOOL "package" FORCE)
+     else("${${${libname}_UPPER}_VERSION_STRING}" STREQUAL "${version}")
+        message(" Not found: ${libname}, incorrect version ( ${${${libname}_UPPER}_VERSION} )")
+        set(${${libname}_UPPER}_FOUND "FALSE")
diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/cxxConfigure-cmake.patch b/var/spack/repos/builtin/packages/bcl2fastq2/cxxConfigure-cmake.patch
new file mode 100644
index 0000000000..4452bb31c1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bcl2fastq2/cxxConfigure-cmake.patch
@@ -0,0 +1,12 @@
+--- a/src/cmake/cxxConfigure.cmake	2017-05-11 16:55:14.745107845 -0700
++++ b/src/cmake/cxxConfigure.cmake	2017-05-11 17:16:39.355981745 -0700
+@@ -101,6 +101,9 @@
+ if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
+   find_package_version(LibXml2 ${BCL2FASTQ_LIBXML2_VERSION})
+   find_package_version(LibXslt ${BCL2FASTQ_LIBXSLT_VERSION})
++  # macro isn't ONLY for redist, see its definition...
++  string(REGEX REPLACE "/include$" "" LIBEXSLT_HINT ${LIBXSLT_INCLUDE_DIR})
++  find_library_redist(LIBEXSLT ${LIBEXSLT_HINT} libexslt/exslt.h exslt)
+ endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
+ 
+ if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py
new file mode 100644
index 0000000000..98799a1444
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py
@@ -0,0 +1,95 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+import shutil
+import llnl.util.tty as tty
+
+
+# This application uses cmake to build, but they wrap it with a
+# configure script that performs dark magic.  This package does it
+# their way.
+class Bcl2fastq2(Package):
+    """The bcl2fastq2 Conversion Software converts base
+       call (BCL) files from a sequencing run into FASTQ
+       files."""
+
+    homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-18.html"
+    url      = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-18-0-12-tar.zip"
+
+    version('2-18-0-12', 'fbe06492117f65609c41be0c27e3215c')
+
+    depends_on('boost@1.54.0')
+    depends_on('cmake@2.8.9:')
+    depends_on('libxml2@2.7.8')
+    depends_on('libxslt@1.1.26~crypto')
+    depends_on('libgcrypt')
+    depends_on('zlib')
+
+    # Their cmake macros don't set the flag when they find a library
+    # that makes them happy.
+    patch('cmake-macros.patch')
+    # After finding the libxslt bits, cmake still needs to wire in the
+    # libexslt bits.
+    patch('cxxConfigure-cmake.patch')
+
+    root_cmakelists_dir = '../src'
+
+    def url_for_version(self, version):
+        url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
+        return url.format(version.dashed)
+
+    # Illumina tucks the source inside a gzipped tarball inside a zip
+    # file.  We let the normal Spack expansion bit unzip the zip file,
+    # then follow it with a function untars the tarball after Spack's
+    # done it's bit.
+    def do_stage(self, mirror_only=False):
+        # wrap (decorate) the standard expand_archive step with a
+        # helper, then call the real do_stage().
+        self.stage.expand_archive = self.unpack_it(self.stage.expand_archive)
+        super(Bcl2fastq2, self).do_stage(mirror_only)
+
+    def unpack_it(self, f):
+        def wrap():
+            f()                 # call the original expand_archive()
+            if os.path.isdir('bcl2fastq'):
+                tty.msg("The tarball has already been unpacked")
+            else:
+                tty.msg("Unpacking bcl2fastq2 tarball")
+                tarball = 'bcl2fastq2-v{0}.tar.gz'.format(self.version.dotted)
+                shutil.move(join_path('spack-expanded-archive', tarball), '.')
+                os.rmdir('spack-expanded-archive')
+                tar = which('tar')
+                tar('-xf', tarball)
+                tty.msg("Finished unpacking bcl2fastq2 tarball")
+        return wrap
+
+    def install(self, spec, prefix):
+        bash = which('bash')
+        bash("src/configure", "--prefix={0}".format(prefix),
+             "--with-cmake={0}".format(join_path(spec['cmake'].prefix.bin,
+                                                 "cmake")))
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/libxslt/package.py b/var/spack/repos/builtin/packages/libxslt/package.py
index 9c5a42bcfb..3396f10242 100644
--- a/var/spack/repos/builtin/packages/libxslt/package.py
+++ b/var/spack/repos/builtin/packages/libxslt/package.py
@@ -36,10 +36,22 @@ class Libxslt(AutotoolsPackage):
     homepage = "http://www.xmlsoft.org/XSLT/index.html"
     url      = "http://xmlsoft.org/sources/libxslt-1.1.28.tar.gz"
 
-    version('1.1.28', '9667bf6f9310b957254fdcf6596600b7')
     version('1.1.29', 'a129d3c44c022de3b9dcf6d6f288d72e')
+    version('1.1.28', '9667bf6f9310b957254fdcf6596600b7')
+    version('1.1.26', 'e61d0364a30146aaa3001296f853b2b9')
+
+    variant('crypto',  default=True,
+            description='Build libexslt with crypto support')
 
     depends_on("libxml2")
     depends_on("xz")
     depends_on("zlib")
-    depends_on("libgcrypt")
+    depends_on("libgcrypt", when="+crypto")
+
+    def configure_args(self):
+        args = []
+        if '~crypto' in self.spec:
+            args.append('--without-crypto')
+        else:
+            args.append('--with-crypto')
+        return args