repeatmodeler: new package at 1.0.11 (#11472)

1 files changed, 66 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/repeatmodeler/package.py b/var/spack/repos/builtin/packages/repeatmodeler/package.py
new file mode 100644
index 0000000000..fa395f4109
--- /dev/null
+++ b/var/spack/repos/builtin/packages/repeatmodeler/package.py
@@ -0,0 +1,66 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Repeatmodeler(Package):
+    """RepeatModeler is a de-novo repeat family identification and modeling
+       package."""
+
+    homepage = "http://www.repeatmasker.org/RepeatModeler/"
+    url      = "http://www.repeatmasker.org/RepeatModeler/RepeatModeler-open-1.0.11.tar.gz"
+
+    version('1.0.11', sha256='7ff0d588b40f9ad5ce78876f3ab8d2332a20f5128f6357413f741bb7fa172193')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-json', type=('build', 'run'))
+    depends_on('perl-uri', type=('build', 'run'))
+    depends_on('perl-lwp', type=('build', 'run'))
+
+    depends_on('repeatmasker', type='run')
+    depends_on('recon+repeatmasker', type='run')
+    depends_on('repeatscout', type='run')
+    depends_on('trf', type='run')
+    depends_on('nseg', type='run')
+    depends_on('ncbi-rmblastn', type='run')
+
+    def install(self, spec, prefix):
+        # like repeatmasker, another interactive installer
+        # questions:
+        #   1. <enter to continue>
+        #   2. <perl path, default is OK>
+        #   3. <source path, default is OK>
+        #   4. RepeatMasker bin path
+        #   5. RECON bin path
+        #   6. RepeatScout bin path
+        #   7. Nseg bin path
+        #   8. trf bin path
+        #   9. Add a search engine:
+        #        1. RMBlast -> Path, Default? (Y/N)
+        #        2. WUBlast/ABBlast -> Path, Default? (Y/N)
+        #        3. Done
+
+        config_answers = [
+            '', '', '',
+            spec['repeatmasker'].prefix.bin,
+            spec['recon'].prefix.bin,
+            spec['repeatscout'].prefix.bin,
+            spec['nseg'].prefix.bin,
+            spec['trf'].prefix.bin,
+            '1', spec['ncbi-rmblastn'].prefix.bin, 'Y',
+            '3',
+        ]
+
+        config_filename = 'spack-config.in'
+
+        with open(config_filename, 'w') as f:
+            f.write('\n'.join(config_answers))
+
+        with open(config_filename, 'r') as f:
+            perl = which('perl')
+            perl('configure', input=f)
+
+        install_tree('.', prefix.bin)