1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
# Copyright 2013-2024 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.package import *
class Mapsplice2(MakefilePackage):
"""MapSplice is a software for mapping RNA-seq data to reference genome
for splice junction discovery that depends only on reference genome,
and not on any further annotations."""
homepage = "http://www.netlab.uky.edu/p/bioinfo/MapSplice2"
url = "https://protocols.netlab.uky.edu/~zeng/MapSplice-v2.2.1.zip"
version("2.2.1", sha256="4f3c1cb49ba0abcfc952de5946ee0b56db28c51f4f4d4f5abca66b4461ca7d05")
patch("Makefile.patch")
patch("mapsplice_ebwt.patch")
depends_on("bowtie")
depends_on("ncurses", type="link")
depends_on("samtools", type="link")
depends_on("python", type="run")
def edit(self, spec, prefix):
for iscan in find(
"src",
["SamRec.*", "AlignmentHandler.cpp", "JunctionHandler.cpp", "FusionSamRec.*"],
recursive=True,
):
m = FileFilter(iscan)
m.filter(r"iscanonical", "iscanonical2")
for makefile in find(".", "[Mm]akefile", recursive=True):
m = FileFilter(makefile)
m.filter("g++", "{0}".format(spack_cxx), string=True)
m.filter(r"CC =.*", "CC = {0}".format(spack_cc))
m.filter(r"CPP =.*", "CPP = {0}".format(spack_cxx))
m.filter(r"CXX =.*", "CXX = {0}".format(spack_cxx))
def install(self, spec, prefix):
install("mapsplice.py", prefix)
install_tree("bin", prefix.bin)
|
