From 65b03a9f03169997042b98670cb44386da43b250 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Tue, 6 Apr 2021 01:48:04 -0500
Subject: trf: add v4.09.1 and other updates (#22782)
- add new version, 4.09.1
- use github url
- convert to autotools package
- deprecate version 4.07b: This version requires manual download and is
a binary only installation.
---
var/spack/repos/builtin/packages/trf/package.py | 31 +++++++++++++++++++++----
1 file changed, 26 insertions(+), 5 deletions(-)
diff --git a/var/spack/repos/builtin/packages/trf/package.py b/var/spack/repos/builtin/packages/trf/package.py
index 1009a14596..79a31be7c5 100644
--- a/var/spack/repos/builtin/packages/trf/package.py
+++ b/var/spack/repos/builtin/packages/trf/package.py
@@ -7,7 +7,7 @@ from spack import *
import os
-class Trf(Package):
+class Trf(AutotoolsPackage):
"""Tandem Repeats Finder is a program to locate and display tandem repeats
in DNA sequences.
@@ -18,13 +18,34 @@ class Trf(Package):
http://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "https://tandem.bu.edu/trf/trf.html"
+ url = "https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.1.tar.gz"
+
+ version('4.09.1', sha256='516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a')
+ version('4.09', sha256='9332155384bef82f6c7c449c038d27f1a14b984b2e93000bfcf125f4d44d6aca')
+
+ # Beginning with version 4.09, trf is open source and available via github.
+ # Only version 4.07b needs to be installed as a binary.
manual_download = True
- version('4.09', '0c594fe666e0332db1df9d160d7fabc8', expand=False,
- url='file://{0}/trf409.linux64'.format(os.getcwd()))
- version('4.07b', sha256='a3a760c7b74c9603fbc08d95e8fa696c00f35a2f179b0bd63b2b13757ad3b471', expand=False,
- url='file://{0}/trf407b.linux64'.format(os.getcwd()))
+ version('4.07b',
+ sha256='a3a760c7b74c9603fbc08d95e8fa696c00f35a2f179b0bd63b2b13757ad3b471',
+ expand=False,
+ url='file://{0}/trf407b.linux64'.format(os.getcwd()),
+ deprecated=True)
+
+ @when('@4.07b')
+ def autoreconf(self, spec, prefix):
+ touch('configure')
+
+ @when('@4.07b')
+ def configure(self, spec, prefix):
+ pass
+
+ @when('@4.07b')
+ def build(self, spec, prefix):
+ pass
+ @when('@4.07b')
def install(self, spec, prefix):
mkdirp(prefix.bin)
--
cgit v1.2.3-70-g09d2