From cf017baa8d9a7121731f13dd900a4929f32534c6 Mon Sep 17 00:00:00 2001
From: snehring <snehring@users.noreply.github.com>
Date: Sat, 5 Aug 2017 12:39:44 -0500
Subject: [PATCH] chlorop: new package (#4865)

* chlorop: new package

* chlorop: moving main script to bin and moving runtime tmp location.

* chlorop: fixing flake8 error.

* chlorop: cleaning up, removing CHLOROTMP, advising user to set it.

* chlorop: removing unused import
---
 .../builtin/packages/chlorop/chlorop.patch    | 36 +++++++++++++
 .../repos/builtin/packages/chlorop/package.py | 53 +++++++++++++++++++
 2 files changed, 89 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/chlorop/chlorop.patch
 create mode 100644 var/spack/repos/builtin/packages/chlorop/package.py

diff --git a/var/spack/repos/builtin/packages/chlorop/chlorop.patch b/var/spack/repos/builtin/packages/chlorop/chlorop.patch
new file mode 100644
index 0000000000..6d49dc53d0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chlorop/chlorop.patch
@@ -0,0 +1,36 @@
+--- a/chlorop	2006-03-20 06:24:22.000000000 -0600
++++ b/chlorop	2017-07-24 10:51:27.000366706 -0500
+@@ -9,8 +9,6 @@
+ STARTDIR=`pwd`
+ 
+ ### GENERAL SETTINGS, CUSTOMIZE +++++++++++++++++++++++++++++++++++++++++++++++
+-# Substitute your chosen location for ChloroP software:
+-CHLOROP=/usr/cbs/packages/chlorop/currdist/chlorop-1.1
+ 
+ # Substitute paste:
+ PASTE=paste
+@@ -43,7 +41,7 @@
+ # other settings:
+ #CHLOROTMPNAME=res`date '+%y%m%d%H%M%S'`.$$
+ CHLOROTMPNAME=res.$$
+-CHLOROTMP=tmp/$CHLOROTMPNAME
++CHLOROTMP=$CHLOROTMP/$CHLOROTMPNAME
+ SCRIPTS=bin
+ SYN=syn
+ ETC=etc
+@@ -80,12 +78,12 @@
+ ### get the infile ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ INFILE=$*
+ 
+-mkdir $CHLOROP/$CHLOROTMP || { echo Cannot create temporary directory; exit 1; }
++mkdir -p $CHLOROTMP || { echo Cannot create temporary directory; exit 1; }
+ 
+ ### prepare input file in HOW and fasta format ++++++++++++++++++++++++++++++++
+ $AWK -f $CHLOROP/$SCRIPTS/in2how+fasta.awk -v informat=$INFORMAT \
+-	-v howout=$CHLOROP/$CHLOROTMP/infile.how \
+-	-v fastaout=$CHLOROP/$CHLOROTMP/infile.fasta $INFILE
++	-v howout=$CHLOROTMP/infile.how \
++	-v fastaout=$CHLOROTMP/infile.fasta $INFILE
+ INFILE=$CHLOROTMP/infile.how
+ 
+ ### change to working directory +++++++++++++++++++++++++++++++++++++++++++++++
diff --git a/var/spack/repos/builtin/packages/chlorop/package.py b/var/spack/repos/builtin/packages/chlorop/package.py
new file mode 100644
index 0000000000..bd5ceda4f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chlorop/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import distutils.dir_util
+import os
+
+
+class Chlorop(Package):
+    """Chlorop predicts the presence of chloroplast transit peptides
+    in protein sequences and the location of potential cTP cleavage
+    sites. You will need to obtain the tarball by visiting the
+    URL and completing the form. You can then either run spack
+    install with the tarball in the directory, or add it to a
+    mirror. You will need to set the CHLOROTMP environment variable
+    to the full path of the directory you want chlorop to use as
+    a temporary directory."""
+
+    homepage = "http://www.cbs.dtu.dk/services/ChloroP/"
+    url      = "file://{0}/chlorop-1.1.Linux.tar.gz".format(os.getcwd())
+
+    version('1.1', 'eb0ba6b28dfa735163ad5fc70e30139e46e33f6ae27f87666a7167a4ac5f71d9')
+
+    depends_on('awk', type='run')
+    patch('chlorop.patch')
+
+    def install(self, spec, prefix):
+        os.rename('chlorop', 'bin/chlorop')
+        distutils.dir_util.copy_tree(".", prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('CHLOROP', self.prefix)