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| author | snehring <7978778+snehring@users.noreply.github.com> | 2023-06-12 03:05:44 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-06-12 10:05:44 +0200 |
| commit | 4cc5e9cac68ba278e33f16f76b48f66bdeb0b470 (patch) | |
| tree | 5674f96e71eeadff869fc0a0f22faf55e4c94379 /var | |
| parent | 41345d18f9fd196354d43d654dfa56a4340473bf (diff) | |
| download | spack-4cc5e9cac68ba278e33f16f76b48f66bdeb0b470.tar.gz spack-4cc5e9cac68ba278e33f16f76b48f66bdeb0b470.tar.bz2 spack-4cc5e9cac68ba278e33f16f76b48f66bdeb0b470.tar.xz spack-4cc5e9cac68ba278e33f16f76b48f66bdeb0b470.zip | |
ltr-retriever 2.9.4 (#38300)
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/ltr-retriever/package.py | 10 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/py-tesorter/package.py | 29 |
2 files changed, 38 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/ltr-retriever/package.py b/var/spack/repos/builtin/packages/ltr-retriever/package.py index 3d1c9c5645..5d5fd52004 100644 --- a/var/spack/repos/builtin/packages/ltr-retriever/package.py +++ b/var/spack/repos/builtin/packages/ltr-retriever/package.py @@ -15,6 +15,9 @@ class LtrRetriever(Package): homepage = "https://github.com/oushujun/LTR_retriever" url = "https://github.com/oushujun/LTR_retriever/archive/v2.8.7.tar.gz" + maintainers("snehring") + + version("2.9.4", sha256="a9f4668113d2d75ab97cd85b456f11b00afd4876848a8ef099622ec0d9e505e7") version("2.8.7", sha256="29ca6f699c57b5e964aa0ee6c7d3e1e4cd5362dadd789e5f0e8c82fe0bb29369") depends_on("perl", type="run") @@ -22,6 +25,7 @@ class LtrRetriever(Package): depends_on("hmmer@3.1b2:", type="run") depends_on("cdhit", type="run") depends_on("repeatmasker", type="run") + depends_on("py-tesorter", type="run", when="@2.9.4:") def install(self, spec, prefix): filter_file(r"BLAST\+=.*", "BLAST+=%s" % spec["blast-plus"].prefix.bin, "paths") @@ -29,8 +33,12 @@ class LtrRetriever(Package): "RepeatMasker=.*", "RepeatMasker=%s" % spec["repeatmasker"].prefix.bin, "paths" ) filter_file("HMMER=.*", "HMMER=%s" % spec["hmmer"].prefix.bin, "paths") - filter_file("CDHIT=.*", "CDHIT=%s" % spec["cdhit"].prefix, "paths") + filter_file("CDHIT=.*", "CDHIT=%s" % spec["cdhit"].prefix.bin, "paths") filter_file("BLAST=.*", "", "paths") + if spec.satisfies("@2.9.4:"): + filter_file( + "^TEsorter=.*$", "TEsorter={}".format(spec["py-tesorter"].prefix.bin), "paths" + ) mkdirp(prefix.opt) mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/py-tesorter/package.py b/var/spack/repos/builtin/packages/py-tesorter/package.py new file mode 100644 index 0000000000..d324cef55f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tesorter/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2023 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 PyTesorter(PythonPackage): + """ + TEsorter is coded for LTR_retriever to classify long terminal repeat + retrotransposons (LTR-RTs) at first. It can also be used to + classify any other transposable elements (TEs), including + Class I and Class II elements which are covered by the + REXdb database. + """ + + homepage = "https://github.com/zhangrengang/TEsorter" + url = "https://github.com/zhangrengang/TEsorter/archive/refs/tags/v1.4.6.tar.gz" + + maintainers("snehring") + + version("1.4.6", sha256="c6952c98fa78d0084742fd6c7d2d1204d36db103c3cbeb19e52093cd9d311523") + + depends_on("py-biopython", type=("build", "run")) + depends_on("py-xopen", type=("build", "run")) + + depends_on("hmmer@3.3:", type="run") + depends_on("blast-plus", type="run") |