summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorJustin S <3630356+codeandkey@users.noreply.github.com>2020-08-06 22:26:52 -0500
committerGitHub <noreply@github.com>2020-08-06 22:26:52 -0500
commit0f8ad5be1bd9d20c1aaf5077512d973b6d6ac6fb (patch)
tree83a0f2c6b6e158720b8f3602f503ede7fef1885d
parent9a7834949d8f9f61c4d4c02e0c1c4804fb94691b (diff)
downloadspack-0f8ad5be1bd9d20c1aaf5077512d973b6d6ac6fb.tar.gz
spack-0f8ad5be1bd9d20c1aaf5077512d973b6d6ac6fb.tar.bz2
spack-0f8ad5be1bd9d20c1aaf5077512d973b6d6ac6fb.tar.xz
spack-0f8ad5be1bd9d20c1aaf5077512d973b6d6ac6fb.zip
isescan: new package at 1.7.2.1 (#16589)
* isescan: new package at 1.7.2.1 * isescan: update external program paths * isescan: use spack compiler
-rw-r--r--var/spack/repos/builtin/packages/isescan/package.py71
1 files changed, 71 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/isescan/package.py b/var/spack/repos/builtin/packages/isescan/package.py
new file mode 100644
index 0000000000..1d4b607046
--- /dev/null
+++ b/var/spack/repos/builtin/packages/isescan/package.py
@@ -0,0 +1,71 @@
+# Copyright 2013-2020 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 Isescan(Package):
+ """A python pipeline to identify IS (Insertion Sequence) elements in
+ genome and metagenome"""
+
+ homepage = "https://github.com/xiezhq/ISEScan"
+ url = "https://github.com/xiezhq/ISEScan/archive/v1.7.2.1.tar.gz"
+
+ version('1.7.2.1', sha256='b971a3e86a8cddaa4bcd520ba9e75425bbe93190466f81a3791ae0cb4baf5e5d')
+
+ depends_on('python@3.3.3:', type='run')
+ depends_on('py-numpy@1.8.0:', type='run')
+ depends_on('py-scipy@0.13.1:', type='run')
+ depends_on('py-biopython@1.62:', type='run')
+ depends_on('py-fastcluster', type='run')
+ depends_on('py-argparse', type='run')
+ depends_on('blast-plus@2.2.31:', type='run')
+ depends_on('fraggenescan@1.30:', type='run')
+ depends_on('hmmer@3.1b2:', type='run')
+
+ def setup_run_environment(self, env):
+ env.prepend_path('PATH', self.prefix)
+ env.prepend_path('LD_LIBRARY_PATH',
+ join_path(self.prefix, 'ssw201507'))
+
+ def install(self, spec, prefix):
+ # build bundled SSW library
+ with working_dir('ssw201507'):
+ Executable(spack_cc)(
+ '-O3', '-pipe', self.compiler.cc_pic_flag, '-shared',
+ '-rdynamic', '-o', 'libssw.' + dso_suffix, 'ssw.c', 'ssw.h',
+ )
+
+ # set paths to required programs
+ blast_pfx = self.spec['blast-plus'].prefix.bin
+ blastn_path = blast_pfx.blastn
+ blastp_path = blast_pfx.blastp
+ makeblastdb_path = blast_pfx.makeblastdb
+
+ hmmer_pfx = self.spec['hmmer'].prefix.bin
+ phmmer_path = hmmer_pfx.phmmer
+ hmmsearch_path = hmmer_pfx.hmmsearch
+
+ fgs_pfx = self.spec['fraggenescan'].prefix.bin
+ fgs_path = join_path(fgs_pfx, 'run_FragGeneScan.pl')
+
+ constants = FileFilter('constants.py')
+
+ constants.filter('/apps/inst/FragGeneScan1.30/run_FragGeneScan.pl',
+ fgs_path, string=True)
+ constants.filter('/apps/inst/hmmer-3.3/bin/phmmer',
+ phmmer_path, string=True)
+ constants.filter('/apps/inst/hmmer-3.3/bin/hmmsearch',
+ hmmsearch_path, string=True)
+ constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/blastn',
+ blastn_path, string=True)
+ constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/blastp',
+ blastp_path, string=True)
+ constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/makeblastdb',
+ makeblastdb_path, string=True)
+
+ # install the whole tree
+ install_tree('.', prefix)
+ set_executable(join_path(prefix, 'isescan.py'))