* [gentoo-commits] proj/sci:jlec commit in: sci-chemistry/shiftx2/, sci-chemistry/shiftx2/files/
@ 2013-06-26 7:09 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2013-06-26 7:09 UTC (permalink / raw
To: gentoo-commits
commit: ad839ff3a63cc6f60e38ca234b01d8452c8bb8a0
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 21 10:44:22 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 21 10:44:22 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ad839ff3
Work in progress
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
...xes.patch => shiftx2-1.07_p20120106-java.patch} | 0
.../files/shiftx2-1.07_p20120106-system.patch | 231 +++++++++++++++++++++
.../shiftx2/shiftx2-1.07_p20120106.ebuild | 30 ++-
3 files changed, 253 insertions(+), 8 deletions(-)
diff --git a/sci-chemistry/shiftx2/files/gentoo-fixes.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch
similarity index 100%
rename from sci-chemistry/shiftx2/files/gentoo-fixes.patch
rename to sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch
diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch
new file mode 100644
index 0000000..764f5ba
--- /dev/null
+++ b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch
@@ -0,0 +1,231 @@
+ natsorted.py | 1 -
+ script/combine_cs.py | 2 +-
+ shiftx2.py | 39 +++++++++++++++++++--------------------
+ shiftx2_util.py | 3 +--
+ shifty3/shifty3.py | 2 +-
+ 5 files changed, 22 insertions(+), 25 deletions(-)
+
+diff --git a/natsorted.py b/natsorted.py
+index 415b393..6fc909e 100755
+--- a/natsorted.py
++++ b/natsorted.py
+@@ -1,4 +1,3 @@
+-#!/usr/bin/env python
+ ############################################################
+ # functions for performing natural sort
+ ############################################################
+diff --git a/script/combine_cs.py b/script/combine_cs.py
+index 4d1dd4f..5182958 100755
+--- a/script/combine_cs.py
++++ b/script/combine_cs.py
+@@ -9,7 +9,7 @@
+ # last updated: Jan 06st, 2012 (by Beomsoo Han)
+ #################################################################################
+ import sys, re, os
+-from natsorted import *
++from shiftx2.natsorted import *
+ from math import exp ## add for new combine rule
+ # from numpy import *
+ tablerows = {} # a hash table for all rows in the table, mapping from residue number to table entry object
+diff --git a/shiftx2.py b/shiftx2.py
+index 0a171c8..72ecbfe 100755
+--- a/shiftx2.py
++++ b/shiftx2.py
+@@ -14,7 +14,7 @@
+ #######################################################################
+ import os, sys, getopt, re, fnmatch
+ from optparse import OptionParser
+-from shiftx2_util import *
++from shiftx2.shiftx2util import *
+
+ DEUTERATED = None
+ NOSHIFTY = None
+@@ -26,7 +26,7 @@ CHAINID = None
+ EXPLICIT = None
+ SHIFTTYPE = None
+
+-SHIFTX2ROOT = ""
++SHIFTX2ROOT = "@GENTOO_PORTAGE_EPREFIX@/opt/shiftx2"
+
+ # temporary file name
+
+@@ -136,8 +136,7 @@ def batch_mode(pattern_str):
+ print "## Running SHIFTX+ modules ..." ## Add by B HAN
+
+ ## switch os.path.abspath("") with SHIFTX2ROOT (set from sys.path[0]) by B HAN
+- cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + \
+- "/lib/weka.jar ShiftXp -b " + "'" + BATCH + "'" + " -atoms " + options.atoms + \
++ cmd_prefix = "jshiftx2" + " -b " + "'" + BATCH + "'" + " -atoms " + options.atoms + \
+ " -ph " + str(options.ph) + " -temp " + str(options.temp)
+ if DEUTERATED:
+ cmd_prefix = cmd_prefix + " -d TRUE"
+@@ -154,14 +153,14 @@ def batch_mode(pattern_str):
+ for infile in pdb_list:
+ # run SHIFTX
+ ## cmd_prefix = "modules/shiftx/shiftx 1 " + os.path.abspath("") + "/" + \
+- cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + infile + " " + infile + ".sx"
++ cmd_prefix = "shiftx 1 " + infile + " " + infile + ".sx"
+ os.system(cmd_prefix)
+ if VERBOSE:
+ print cmd_prefix
+ # convert from table format to CSV
+ ## cmd_prefix = "python script/shiftx2shiftxp.py " + os.path.abspath("") + "/" + \
+ ## infile + ".sx " + os.path.abspath("") + "/" + infile + ".sxp"
+- cmd_prefix = "python "+ SHIFTX2ROOT +"/script/shiftx2shiftxp.py " + \
++ cmd_prefix = "shiftx2shiftxp.py " + \
+ infile + ".sx " + infile + ".sxp"
+ ## switched by B HAN
+ ## infile + ".sx " + os.path.abspath("") + "/" + infile.split('.')[0] + ".sxp"
+@@ -180,7 +179,7 @@ def batch_mode(pattern_str):
+ ## os.chdir(os.path.abspath("shifty3"))
+ sys.path.append(SHIFTX2ROOT+"/shifty3")
+ os.chdir(SHIFTX2ROOT+"/shifty3")
+- shifty_cmd = "python shifty3.py -i " + \
++ shifty_cmd = "shifty3.py -i " + \
+ infile + " -o " + infile + ".shifty -c 40 "
+ if DEUTERATED:
+ shifty_cmd = shifty_cmd + " -d"
+@@ -207,7 +206,7 @@ def batch_mode(pattern_str):
+ errmsg = "Error: SHIFTX+ cannot make a prediction file."
+ return errmsg
+
+- combine_cmd = "python " + SHIFTX2ROOT +"/script/combine_cs.py " + sx_outfile + " " + infile + ".shifty "
++ combine_cmd = "combine_cs.py " + sx_outfile + " " + infile + ".shifty "
+ if not options.outfile:
+ combine_cmd = combine_cmd + infile + ".cs"
+ else:
+@@ -248,7 +247,7 @@ def model_batch(pattern_str):
+ # run shiftx1 or shiftx+
+ if not SHIFTX1:
+ # run SHIFTX+
+- cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + "/lib/weka.jar ShiftXp -b " + \
++ cmd_prefix = "jshiftx2 -b " + \
+ "'" + pattern_str + "'" + " -atoms " + options.atoms + \
+ " -ph " + str(options.ph) + " -temp " + str(options.temp)
+ if DEUTERATED:
+@@ -263,14 +262,14 @@ def model_batch(pattern_str):
+ else:
+ for infile in pdb_list:
+ # run SHIFTX
+- cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + infile + \
++ cmd_prefix = "shiftx 1 " + infile + \
+ " " + infile + ".sx"
+ os.system(cmd_prefix)
+ if VERBOSE:
+ print cmd_prefix
+
+ # convert from table format to CSV
+- cmd_prefix = "python "+ SHIFTX2ROOT +"/script/shiftx2shiftxp.py " + \
++ cmd_prefix = "shiftx2shiftxp.py " + \
+ infile + ".sx " + infile + ".sxp"
+
+ os.system(cmd_prefix)
+@@ -328,7 +327,7 @@ def nmr_mode(infile, obs_cs):
+ if not NOSHIFTY:
+ sys.path.append( SHIFTX2ROOT + "/shifty3")
+ os.chdir(SHIFTX2ROOT + "/shifty3")
+- shifty_cmd = "python shifty3.py -i " + infile + \
++ shifty_cmd = "shifty3.py -i " + infile + \
+ " -o " + infile + ".shifty -c 40 "
+ if DEUTERATED:
+ shifty_cmd = shifty_cmd + " -d"
+@@ -350,7 +349,7 @@ def nmr_mode(infile, obs_cs):
+ return errmsg
+
+ # combine result
+- combine_cmd = "python "+ SHIFTX2ROOT + "/script/combine_cs.py " + infile_prefix + ".sxp " + infile + ".shifty "
++ combine_cmd = "combine_cs.py " + infile_prefix + ".sxp " + infile + ".shifty "
+ if not options.outfile:
+ combine_cmd = combine_cmd + infile + ".cs"
+ ## add by B HAN; if it does not exist, error message will occur
+@@ -367,7 +366,7 @@ def nmr_mode(infile, obs_cs):
+ # should be accomplished in a function
+ if obs_cs!= None:
+ # calculate correlation
+- cmd = "python " + SHIFTX2ROOT +"/script/model_corr.py " + obs_cs + " " + infile_prefix + ".modelcorr " + ' '.join(model_outfiles)
++ cmd = "model_corr.py " + obs_cs + " " + infile_prefix + ".modelcorr " + ' '.join(model_outfiles)
+ os.system(cmd)
+
+ # plot correlation graphs, plot line graph but no barplots
+@@ -456,7 +455,7 @@ def single_mode(infile, outfile):
+
+ if not SHIFTX1:
+ # run SHIFTX+
+- cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + "/lib/weka.jar ShiftXp -i " + inputfile \
++ cmd_prefix = "jshiftx2 -i " + inputfile \
+ + " -atoms " + options.atoms + " -ph " + str(options.ph) + " -temp " + str(options.temp)
+ if DEUTERATED:
+ cmd_prefix = cmd_prefix + " -d TRUE"
+@@ -476,12 +475,12 @@ def single_mode(infile, outfile):
+ sys.exit(-1)
+ else:
+ # run SHIFTX
+- cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + inputfile + " " + sx1_outfile
++ cmd_prefix = "shiftx 1 " + inputfile + " " + sx1_outfile
+ os.system(cmd_prefix)
+ if VERBOSE:
+ print cmd_prefix
+ # convert from table format to CSV
+- cmd_prefix = "python " + SHIFTX2ROOT + "/script/shiftx2shiftxp.py " + sx1_outfile + " " + sxp_outfile
++ cmd_prefix = "shiftx2shiftxp.py " + sx1_outfile + " " + sxp_outfile
+ os.system(cmd_prefix)
+ if VERBOSE:
+ print cmd_prefix
+@@ -490,7 +489,7 @@ def single_mode(infile, outfile):
+ if not NOSHIFTY:
+ sys.path.append(SHIFTX2ROOT + "/shifty3")
+ os.chdir(SHIFTX2ROOT +"/shifty3")
+- shifty_cmd = "python shifty3.py -i " + inputfile + " -o " + sy_outfile + " -c 40 "
++ shifty_cmd = "shifty3.py -i " + inputfile + " -o " + sy_outfile + " -c 40 "
+ if DEUTERATED:
+ shifty_cmd = shifty_cmd + " -d"
+ if VERBOSE:
+@@ -513,7 +512,7 @@ def single_mode(infile, outfile):
+ return errmsg
+
+ # combine result
+- combine_cmd = "python script/combine_cs.py " + sxp_outfile + " " + sy_outfile + " "
++ combine_cmd = "combine_cs.py " + sxp_outfile + " " + sy_outfile + " "
+ combine_cmd = combine_cmd + outfile # specify output file name
+
+ combine_cmd = add_atom_format_option(combine_cmd)
+@@ -543,7 +542,7 @@ def cleanup_tempfiles(files):
+ if __name__ == '__main__':
+ print "## SHIFTX2 Ver 1.07 (Released 4 Jan. 2012) ##"
+
+- SHIFTX2ROOT = sys.path[0]
++ #SHIFTX2ROOT = sys.path[0]
+
+ #if len(sys.argv)<3:
+ # print "Usage: python shiftx2_main.py [input.pdb] [-atoms: all]"
+diff --git a/shiftx2_util.py b/shiftx2_util.py
+index d357a8e..6ce5e6c 100755
+--- a/shiftx2_util.py
++++ b/shiftx2_util.py
+@@ -1,4 +1,3 @@
+-#!/usr/bin/env python
+ ####################################################################
+ # shiftx2_util.py: utility functions supporting shiftx2_main.py
+ #
+@@ -6,7 +5,7 @@
+ # date: April 13th, 2011
+ ####################################################################
+ import sys, os
+-from natsorted import *
++from shiftx2.natsorted import *
+
+ # FUNCTIONS FOR SPLITING PDB FILE WITH MULTIPLE NMR MODELS
+
+diff --git a/shifty3/shifty3.py b/shifty3/shifty3.py
+index 796af32..9360b87 100755
+--- a/shifty3/shifty3.py
++++ b/shifty3/shifty3.py
+@@ -12,7 +12,7 @@ import sys, os, re, datetime, time
+ ###############################################################
+ # path for xalign and blast executibles and blast databases
+ XALIGN_EXE = "xalign_x" # executable for xalign
+-BLASTP_EXE = "./blast/bin/blastall -p blastp" # executable for blast
++BLASTP_EXE = "blastall -p blastp" # executable for blast
+
+ BLASTDB = "blastdb" # folder containing the blast database
+ SHIFTDB = "refdb" # folder containing the BMRB shift database
diff --git a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
index 5a19e4b..01ebe04 100644
--- a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
+++ b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
@@ -6,7 +6,7 @@ EAPI=5
PYTHON_COMPAT=( python{2_6,2_7} )
-inherit java-pkg-2 java-pkg-simple python-r1 versionator
+inherit java-pkg-2 java-pkg-simple prefix python-r1 versionator
MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))"
MY_PATCH="20120106"
@@ -25,6 +25,7 @@ CDEPEND="dev-util/weka"
RDEPEND="${CDEPEND}
dev-lang/R
+ sci-biology/ncbi-tools
sci-chemistry/reduce
>=virtual/jre-1.5"
DEPEND="${CDEPEND}
@@ -35,10 +36,13 @@ S="${WORKDIR}"/${MY_P}
QA_PREBUILT="/opt/.*"
src_prepare() {
- epatch "${FILESDIR}/gentoo-fixes.patch"
+ epatch \
+ "${FILESDIR}"/${P}-java.patch \
+ "${FILESDIR}"/${P}-system.patch
+
rm "${S}"/src/FeatureRanges.java || die
- shared=$(echo "/usr/share/${PN}" | sed -e 's/\//\\\//g')
+ shared=$(echo "${EPREFIX}/usr/share/${PN}" | sed -e 's/\//\\\//g')
sed -i -e "s/PUT_GENTOO_SHARE_PATH_HERE/${shared}/g" "${S}/src/ShiftXp.java" || die
if use debug; then
@@ -52,6 +56,8 @@ src_prepare() {
-i modules/*/Makefile || die
sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
+
+ eprefixify ${PN}.py
}
src_compile() {
@@ -78,7 +84,7 @@ src_compile() {
src_install() {
java-pkg_dojar "${PN}.jar"
- java-pkg_dolauncher ${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin"
+ java-pkg_dolauncher j${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin"
insinto /usr/share/${PN}
doins "${S}"/lib/{limitedcshift.dat,RandomCoil.csv,data-header.arff}
@@ -89,7 +95,11 @@ src_install() {
local instdir="/opt/${PN}"
dodoc README 1UBQ.pdb
- python_parallel_foreach_impl python_doscript "${S}"/*py
+ python_parallel_foreach_impl python_newscript ${PN}.py ${PN}
+ mv shiftx2_util.py shiftx2util.py || die
+ python_moduleinto ${PN}
+ touch __init__.py
+ python_parallel_foreach_impl python_domodule natsorted.py shiftx2util.py __init__.py
# other modules
dobin \
@@ -98,15 +108,19 @@ src_install() {
"${S}"/modules/effects/caleffect
# script
- python_scriptinto ${instdir}/script
python_parallel_foreach_impl python_doscript "${S}"/script/*py
exeinto ${instdir}/script
doexe "${S}"/script/*.r
# shifty3
- python_scriptinto ${instdir}/shifty3
- python_parallel_foreach_impl python_doscript "${S}"/shifty3/*py
+ python_parallel_foreach_impl python_newscript "${S}"/shifty3/*py shifty3
exeinto ${instdir}/shifty3
doexe "${S}"/shifty3/xalign_x
dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x
+
+ insinto ${instdir}/shifty3
+ doins -r "${S}"/shifty3/{blastdb,refdb,xalign.parms,wt.rbo}
+
+ python_parallel_foreach_impl python_doscript "${S}"/shifty3/utils/*py
+ dobin "${S}"/shifty3/utils/create_blastdb.sh
}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: sci-chemistry/shiftx2/, sci-chemistry/shiftx2/files/
@ 2013-06-26 7:09 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2013-06-26 7:09 UTC (permalink / raw
To: gentoo-commits
commit: 4e927f101d6f9623ea73756cf65d2d9df3a6533d
Author: Johann Schmitz <johann <AT> j-schmitz <DOT> net>
AuthorDate: Fri Jun 21 13:45:51 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 21 13:45:51 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4e927f10
Completly removed the directory check in the java source (we have everything under control in gentoo).
Removed the .py extension from the -system.patch to make that part working again (it's installed without extensions to /usr/bin/!).
Package-Manager: portage-2.1.12.2
---
sci-chemistry/shiftx2/ChangeLog | 8 +++-
.../files/shiftx2-1.07_p20120106-java.patch | 45 +++++++++++++++++++---
.../files/shiftx2-1.07_p20120106-system.patch | 6 +--
3 files changed, 49 insertions(+), 10 deletions(-)
diff --git a/sci-chemistry/shiftx2/ChangeLog b/sci-chemistry/shiftx2/ChangeLog
index 5aafaf3..572650b 100644
--- a/sci-chemistry/shiftx2/ChangeLog
+++ b/sci-chemistry/shiftx2/ChangeLog
@@ -2,7 +2,13 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 Jun 2013; johann@j-schmitz.net files/shiftx2-1.07_p20120106-java.patch,
+ files/shiftx2-1.07_p20120106-system.patch:
+ Completly removed the directory check in the java source (we have everything
+ under control in gentoo). Removed the .py extension from the -system.patch to
+ make that part working again (it's installed without extensions to
+ /usr/bin/!).
+
16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx2-1.07_p20120106.ebuild,
metadata.xml:
Respect FLAGS
-
diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch
index 2baa443..ea64cea 100644
--- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch
+++ b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch
@@ -182,13 +182,46 @@ index 505a3f6..920f420 100755
// Loading only one time, that's why these are here
static RandomCoil rcoil = new RandomCoil();
static LimitedCShift chkcshift = new LimitedCShift();
-@@ -140,8 +140,7 @@ public class ShiftXp {
+@@ -41,7 +41,7 @@ public class ShiftXp {
+ buf.append("Detail information: http://www.shiftx2.ca or http://redpoll.pharmacy.ualberta.ca\n");
+ buf.append("--------------------------------------------------------------------------------\n\n");
+
+- buf.append("SYNOPSIS\n\t java -Xmx1500m -cp <SHIFTX+ dir>/bin:<SHIFTX+ dir>/lib/weka.jar ShiftXp [options]\n");
++ buf.append("SYNOPSIS\n\t jshiftx2 [options]\n");
+
+ buf.append("OPTIONS:\n");
+ buf.append("\t -i [<directory/> infile.pdb | ALLPDB]\n");
+@@ -54,10 +54,10 @@ public class ShiftXp {
+ buf.append("\t -temp <number> Temperature, default=298\n");
+ buf.append("\t -d [TRUE | FALSE] Deuterated pdb, default=FALSE \n");
+ buf.append("\t -r [TRUE | FALSE] Print randon coild shift (only for CSV format), default=FALSE \n");
+- buf.append("\t -dir <SHIFTX+ directory> The installed directory of SHIFTX+/SHIFTX2\n\n");
++// buf.append("\t -dir <SHIFTX+ directory> The installed directory of SHIFTX+/SHIFTX2\n\n");
+
+ buf.append("EXAMPLE:\n");
+- buf.append("\t java -Xmx1500m -cp ~/shiftx2/bin:~/shiftx2/lib/weka.jar ShiftXp -i 1ubq.pdb\n\n");
++ buf.append("\t jshiftx2 -i 1ubq.pdb\n\n");
+ buf.append("\n");
+
+ System.out.println( buf );
+@@ -138,20 +138,6 @@ public class ShiftXp {
+ }
+ }
- // check execute directory
- // 2011.08.31 changed shiftx2_main.py --> shiftx2.py
+- // check execute directory
+- // 2011.08.31 changed shiftx2_main.py --> shiftx2.py
- if ( !( new File( SHIFTX2_DIR + "/shiftx2.py").exists()
- && new File(SHIFTX2_DIR + "/lib/weka.jar").exists() ) ) {
-+ if (!new File(SHIFTX2_DIR + "/shiftx2.py").exists()) {
-
+-
+- System.err.println("\n********************************************************************************");
+- System.err.println("[Error]\t Required: When the SHIFTX2 execute on other directory,\n"
+- +"\t it should be set as a parameter. Use '-dir' option.");
+- System.err.println("> Current directory: "+System.getProperty("user.dir"));
+- System.err.println("********************************************************************************\n");
+-
+- usage();
+- }
+-
+ if ( inPDBFile == null || inPDBFile.length() < 1) {
System.err.println("\n********************************************************************************");
- System.err.println("[Error]\t Required: When the SHIFTX2 execute on other directory,\n"
+ System.err.println("[Error] Required: There is no input PDB filename.");
diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch
index 764f5ba..7625f74 100644
--- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch
+++ b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch
@@ -81,7 +81,7 @@ index 0a171c8..72ecbfe 100755
sys.path.append(SHIFTX2ROOT+"/shifty3")
os.chdir(SHIFTX2ROOT+"/shifty3")
- shifty_cmd = "python shifty3.py -i " + \
-+ shifty_cmd = "shifty3.py -i " + \
++ shifty_cmd = "shifty3 -i " + \
infile + " -o " + infile + ".shifty -c 40 "
if DEUTERATED:
shifty_cmd = shifty_cmd + " -d"
@@ -125,7 +125,7 @@ index 0a171c8..72ecbfe 100755
sys.path.append( SHIFTX2ROOT + "/shifty3")
os.chdir(SHIFTX2ROOT + "/shifty3")
- shifty_cmd = "python shifty3.py -i " + infile + \
-+ shifty_cmd = "shifty3.py -i " + infile + \
++ shifty_cmd = "shifty3 -i " + infile + \
" -o " + infile + ".shifty -c 40 "
if DEUTERATED:
shifty_cmd = shifty_cmd + " -d"
@@ -176,7 +176,7 @@ index 0a171c8..72ecbfe 100755
sys.path.append(SHIFTX2ROOT + "/shifty3")
os.chdir(SHIFTX2ROOT +"/shifty3")
- shifty_cmd = "python shifty3.py -i " + inputfile + " -o " + sy_outfile + " -c 40 "
-+ shifty_cmd = "shifty3.py -i " + inputfile + " -o " + sy_outfile + " -c 40 "
++ shifty_cmd = "shifty3 -i " + inputfile + " -o " + sy_outfile + " -c 40 "
if DEUTERATED:
shifty_cmd = shifty_cmd + " -d"
if VERBOSE:
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2013-06-26 7:09 [gentoo-commits] proj/sci:jlec commit in: sci-chemistry/shiftx2/, sci-chemistry/shiftx2/files/ Justin Lecher
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2013-06-26 7:09 Justin Lecher
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