From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 710C51381F3 for ; Wed, 26 Jun 2013 07:10:08 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 24BB8E0A72; Wed, 26 Jun 2013 07:09:57 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 41296E0A6A for ; Wed, 26 Jun 2013 07:09:56 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 31AF033E73C for ; Wed, 26 Jun 2013 07:09:55 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id CD148E5463 for ; Wed, 26 Jun 2013 07:09:53 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1371822351.4e927f101d6f9623ea73756cf65d2d9df3a6533d.jlec@gentoo> Subject: [gentoo-commits] proj/sci:jlec commit in: sci-chemistry/shiftx2/, sci-chemistry/shiftx2/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/shiftx2/ChangeLog sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch X-VCS-Directories: sci-chemistry/shiftx2/ sci-chemistry/shiftx2/files/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 4e927f101d6f9623ea73756cf65d2d9df3a6533d X-VCS-Branch: jlec Date: Wed, 26 Jun 2013 07:09:53 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: a6d39dea-7047-47c0-b05b-7371d4d97063 X-Archives-Hash: a1926fcc2e632e5f7341c5a3f7869cc1 commit: 4e927f101d6f9623ea73756cf65d2d9df3a6533d Author: Johann Schmitz j-schmitz net> AuthorDate: Fri Jun 21 13:45:51 2013 +0000 Commit: Justin Lecher gentoo 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 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 /bin:/lib/weka.jar ShiftXp [options]\n"); ++ buf.append("SYNOPSIS\n\t jshiftx2 [options]\n"); + + buf.append("OPTIONS:\n"); + buf.append("\t -i [ infile.pdb | ALLPDB]\n"); +@@ -54,10 +54,10 @@ public class ShiftXp { + buf.append("\t -temp 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 The installed directory of SHIFTX+/SHIFTX2\n\n"); ++// buf.append("\t -dir 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: