Package/mirdeep/fix for new url take2 (#8247)

* rename: mirdeep -> mirdeep2 * fixes for new url
2018-05-23 05:25:42 -07:00
parent 3712ac1f66
commit bc73e85af8
1 changed files with 4 additions and 4 deletions
--- a/var/spack/repos/builtin/packages/mirdeep2/package.py
+++ b/var/spack/repos/builtin/packages/mirdeep2/package.py
@@ -0,0 +1,67 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 glob
+
+
+class Mirdeep2(Package):
+    """miRDeep2 is a completely overhauled tool which discovers microRNA genes
+       by analyzing sequenced RNAs."""
+
+    homepage = "https://www.mdc-berlin.de/8551903/en/"
+    url      = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip"
+
+    version('0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-pdf-api2', type=('build', 'run'))
+    depends_on('bowtie')
+    depends_on('viennarna')
+    depends_on('squid')
+    depends_on('randfold')
+
+    def url_for_version(self, version):
+        url = 'https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_{0}.zip'
+        return url.format(version.underscored)
+
+    def patch(self):
+        with working_dir('src'):
+            files = glob.iglob("*.pl")
+            for file in files:
+                change = FileFilter(file)
+                change.filter('usr/bin/perl', 'usr/bin/env perl')
+                change.filter('perl -W', 'perl')
+                change.filter("../Rfam_for_miRDeep.fa",
+                              "Rfam_for_miRDeep.fa")
+                change.filter("../install_successful",
+                              "install_successful")
+
+    def install(self, spec, prefix):
+        install_tree('src', prefix.bin)
+        install('Rfam_for_miRDeep.fa', prefix.bin)
+        # miRDeep looks for the install_sucessful file to check if you used
+        # their automated install script which we'll just be kind of hacking
+        # around
+        touch(prefix.bin.install_successful)