Merge branch 'ercpe'

* ercpe:
  sci-chemistry/shiftx2: Respect FLAGS
  Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the emake part (portage complains about LDFLAGS not respected), but should work.
  broken ebuild for java fixing Signed-off-by: Justin Lecher <jlec@gentoo.org>

5 files changed, 354 insertions, 0 deletions

diff --git a/sci-chemistry/shiftx2/ChangeLog b/sci-chemistry/shiftx2/ChangeLog
new file mode 100644
index 000000000..5aafaf3ca
--- /dev/null
+++ b/sci-chemistry/shiftx2/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-chemistry/shiftx2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx2-1.07_p20120106.ebuild,
+  metadata.xml:
+  Respect FLAGS
+
diff --git a/sci-chemistry/shiftx2/Manifest b/sci-chemistry/shiftx2/Manifest
new file mode 100644
index 000000000..94fd67e47
--- /dev/null
+++ b/sci-chemistry/shiftx2/Manifest
@@ -0,0 +1 @@
+DIST shiftx2-v107-linux-20120106.tgz 114164215 SHA256 47bd11f00c824967738f72a02387b47eafc60a10697aa157e27163f2edbf9927 SHA512 b1fa6ce19e988a938e6645fdbd14f7903b4db13754a476c67da0bf74909675e07b7cec4df63be30d7190ea645e8822eef551e6dd26625172e585da279f1f7396 WHIRLPOOL 20fc5ea052106e2f6f708ba61da2ad9310a50a1c85dfb46d947c919d665835cc43180267094c057b7ce542b59659a1b44940c762c4c8e190cdbb7727dc30c865
diff --git a/sci-chemistry/shiftx2/files/gentoo-fixes.patch b/sci-chemistry/shiftx2/files/gentoo-fixes.patch
new file mode 100644
index 000000000..2baa443c5
--- /dev/null
+++ b/sci-chemistry/shiftx2/files/gentoo-fixes.patch
@@ -0,0 +1,194 @@
+diff --git a/shiftx2-v107-linux/src/LimitedCShift.java b/shiftx2-v107-linux/src/LimitedCShift.java
+index cd27fbf..9e72208 100755
+--- a/shiftx2-v107-linux/src/LimitedCShift.java
++++ b/shiftx2-v107-linux/src/LimitedCShift.java
+@@ -13,8 +13,8 @@ public class LimitedCShift {
+ 	public void loadLimitedCShift () {		
+                 // System.out.println("SHIFTX2_DIR: "+ShiftXp.SHIFTX2_DIR);
+ 
+-		String filename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.dat";
+-		String objFilename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.osf";
++		String filename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.dat";
++		String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.osf";
+ 		
+ 		File f = new File(objFilename);
+ 		if (f.exists()) {
+@@ -44,7 +44,7 @@ public class LimitedCShift {
+ 				br.close();
+ 				
+ 				// save object into object file format for speed up
+-				saveObjectFile(objFilename, limshift);
++				//saveObjectFile(objFilename, limshift);
+ 
+ 			} catch(IOException ex){
+ 				ex.printStackTrace();
+diff --git a/shiftx2-v107-linux/src/ModuleExecutor.java b/shiftx2-v107-linux/src/ModuleExecutor.java
+index 36cfeb1..704451f 100755
+--- a/shiftx2-v107-linux/src/ModuleExecutor.java
++++ b/shiftx2-v107-linux/src/ModuleExecutor.java
+@@ -22,12 +22,12 @@ public class ModuleExecutor {
+ 	// private static final String WORKING_DIR = "./wkdir/";
+ 	private static String WORKING_DIR = "";
+ 
+-	private static final String RESMF_EXE = "/modules/resmf/resmf";
+-	private static final String EFFECTS_EXE = "/modules/effects/caleffect"; 
+-	private static final String ANGLES_EXE = "/modules/angles/get_angles";	
+-	private static final String ANGLES_REDUCE_DIR = "/modules/angles";
++	private static final String RESMF_EXE = "resmf";
++	private static final String EFFECTS_EXE = "caleffect"; 
++	private static final String ANGLES_EXE = "get_angles";	
++	private static final String ANGLES_REDUCE_DIR = "angles";
+ 
+-    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
++//    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
+ 
+ 	private static final String REDUCE_FLAG = "1"; // 1 or 0
+ 
+@@ -80,8 +80,8 @@ public class ModuleExecutor {
+ 		if(DEBUG) System.out.println("> Processing [Major Features] with " + pdbfile);
+         // Update: add pdbdir both input pdbfile and output result, pdbId (2011.03.17)
+ 		// cmd = RESMF_EXE + " -f " + pdbdir +"/"+ pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf";
+-		cmd = SHIFTXP_DIR + RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" 
+-                      + " -d " + SHIFTXP_DIR + "/modules/resmf/lib";
++		cmd = RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" 
++                      + " -d " + ShiftXp.GENTOO_SHARE_PATH + "/vader";
+ 
+ 		if(DEBUG){ System.out.println("\t"+cmd); }
+ 		execCode = execute_command(cmd); 
+@@ -93,7 +93,7 @@ public class ModuleExecutor {
+ 		
+ 		/* call effects for calculating ring current calculator */
+ 		if(DEBUG) System.out.println("> processing [Effects] with " + pdbfile);
+-		cmd = SHIFTXP_DIR + EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy";
++		cmd = EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy";
+ 
+ 		if(DEBUG){ System.out.println("\t"+cmd); }
+ 		execCode = execute_command(cmd); 
+@@ -106,7 +106,7 @@ public class ModuleExecutor {
+ 		/* call angle calculator : output must be redirected to file using PrintStream */
+ 		if(DEBUG) System.out.println("> Processing [Angle] with " + pdbfile);
+ 		// cmd = ANGLES_EXE + " " + ANGLES_REDUCE_DIR + " " + pdbfile ;
+-		cmd = SHIFTXP_DIR + ANGLES_EXE + " " + SHIFTXP_DIR + ANGLES_REDUCE_DIR + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG;
++		cmd = ANGLES_EXE + " " + ShiftXp.GENTOO_SHARE_PATH + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG;
+ 		String outpath = WORKING_DIR + pdbId + ".angles";
+ 
+ 		if(DEBUG){ System.out.println("\t"+cmd); }
+diff --git a/shiftx2-v107-linux/src/PredictionModels.java b/shiftx2-v107-linux/src/PredictionModels.java
+index a77d1cb..fb84666 100755
+--- a/shiftx2-v107-linux/src/PredictionModels.java
++++ b/shiftx2-v107-linux/src/PredictionModels.java
+@@ -13,9 +13,7 @@ public class PredictionModels {
+     private final static String MODEL_FILE_SIDECHAIN_ONLY = "predmodels_sidechain.sobj";
+ 
+     private final static String OBJECT_MODEL_DIRECTORY = "/lib";
+-    private final static String MODEL_DIRECTORY = "/lib/predmodels";
+-
+-    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
++    private final static String MODEL_DIRECTORY = "predmodels";
+ 
+     HashMap<String, Classifier> hsmap_predmodel = new HashMap<String, Classifier>();
+ 
+@@ -36,7 +34,7 @@ public class PredictionModels {
+        // System.out.println("SHIFTXP_DIR:" + SHIFTXP_DIR+"\n\n");
+        // System.out.println("SHIFTX2_DIR:" + ShiftXp.SHIFTX2_DIR+"\n\n");
+ 
+-        String headerfilename = ShiftXp.SHIFTX2_DIR + "/lib/data-header.arff"; 
++        String headerfilename = ShiftXp.GENTOO_SHARE_PATH + "/data-header.arff"; 
+ 
+         try {
+             // assigned instance header from data-header.arff
+@@ -150,7 +148,7 @@ public class PredictionModels {
+             // if option is not sidechain only, put backbone models into modeling file 
+             if ( ! this.prediction_type.equals("SIDECHAIN") ) {
+                 for(int i=0; i < BACKBONE_MODEL_LENGTH; i++)  {
+-                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
++                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
+                     classifier = (Classifier) ois.readObject();
+                     hsmap_predmodel.put(atomNameArray[i],classifier);
+                     ois.close();
+@@ -160,7 +158,7 @@ public class PredictionModels {
+             // if option is not backbone only, put/append sidechain models into modeling file
+             if ( ! this.prediction_type.equals("BACKBONE") ) {
+                 for(int i=BACKBONE_MODEL_LENGTH; i < (BACKBONE_MODEL_LENGTH + SIDECHAIN_MODEL_LENGTH); i++)  {
+-                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
++                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
+                     classifier = (Classifier) ois.readObject();
+                     hsmap_predmodel.put(atomNameArray[i], classifier);
+                     ois.close();
+@@ -185,11 +183,11 @@ public class PredictionModels {
+         */
+ 
+         if ( this.prediction_type.equals("ALL") == true) {
+-            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_ALLATOMS;
++            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_ALLATOMS;
+         } else if ( this.prediction_type.equals("BACKBONE") == true) {
+-            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_BACKBONE_ONLY;
++            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_BACKBONE_ONLY;
+         } else if ( this.prediction_type.equals("SIDECHAIN") == true) {
+-            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_SIDECHAIN_ONLY;
++            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_SIDECHAIN_ONLY;
+         } 
+ 
+         File f = new File( model_file );
+@@ -198,7 +196,7 @@ public class PredictionModels {
+             readHashObjectPredModelFile( model_file );
+         } else {
+             setHashMap(); 
+-            saveHashObjectPredModelFile( model_file ); 
++//            saveHashObjectPredModelFile( model_file ); 
+         }
+     }
+ 
+diff --git a/shiftx2-v107-linux/src/RandomCoil.java b/shiftx2-v107-linux/src/RandomCoil.java
+index 25a8999..7442938 100755
+--- a/shiftx2-v107-linux/src/RandomCoil.java
++++ b/shiftx2-v107-linux/src/RandomCoil.java
+@@ -33,11 +33,9 @@ public class RandomCoil {
+ 	public void loadRandomCoil() {		
+ 
+         // change path as absolute path
+-        String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
+-
+-		String filename = SHIFTXP_DIR + "/lib/RandomCoil.csv";
+-		String objFilename = SHIFTXP_DIR + "/lib/RandomCoil.osf";
+-		String objAtomListname = SHIFTXP_DIR + "/lib/RCoilAtomlist.osf";
++		String filename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.csv";
++		String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.osf";
++		String objAtomListname = ShiftXp.GENTOO_SHARE_PATH + "/RCoilAtomlist.osf";
+ 		
+ 		
+ 		File f = new File(objFilename);
+@@ -85,8 +83,8 @@ public class RandomCoil {
+ 				br.close();
+ 				
+ 				// save object into object file format for speed up
+-				saveObjectFile(objFilename, rcoil);				
+-				saveObjectFile(objAtomListname, restypeAtomStringList);
++//				saveObjectFile(objFilename, rcoil);				
++//				saveObjectFile(objAtomListname, restypeAtomStringList);
+ 
+ 			} catch(IOException ex){
+ 				ex.printStackTrace();
+diff --git a/shiftx2-v107-linux/src/ShiftXp.java b/shiftx2-v107-linux/src/ShiftXp.java
+index 505a3f6..920f420 100755
+--- a/shiftx2-v107-linux/src/ShiftXp.java
++++ b/shiftx2-v107-linux/src/ShiftXp.java
+@@ -27,7 +27,7 @@ public class ShiftXp {
+     static final boolean DEBUG = false; 
+     static boolean RCOIL_PRINTOUT = false;
+     static String SHIFTX2_DIR = ".";  // to support running on other directory
+-
++    public static final String GENTOO_SHARE_PATH = "PUT_GENTOO_SHARE_PATH_HERE";
+     // 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 {
+ 
+         // 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"
diff --git a/sci-chemistry/shiftx2/metadata.xml b/sci-chemistry/shiftx2/metadata.xml
new file mode 100644
index 000000000..80444f44b
--- /dev/null
+++ b/sci-chemistry/shiftx2/metadata.xml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <longdescription>
+		SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical
+		shifts for proteins using their structural (PDB) coordinates as input.
+		SHIFTX2 combines ensemble machine learning methods with sequence
+		alignment-based methods to calculate protein chemical shifts for
+		backbone
+		and side chain atoms. SHIFTX2 has been trained on a carefully selected
+		set of
+		197 proteins and tested on a separate set of 61 proteins. Both the
+		training
+		and testing sets consisted of high resolution X-ray structures (less
+		2.1A)
+		with carefully verified chemical shifts assignments. SHIFTX2 is able to
+		attain
+		correlation coefficients between experimentally observed and predicted
+		backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB),
+		0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412,
+		0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to
+		other
+		chemical shift predictors using the same testing data set indicates that
+		SHIFTX2 is substantially more accurate (up to 26% better by
+		correlation
+		coefficient with an RMS error that is up to 3.3X smaller) than any other
+		program.
+
+		Please cite the following: Beomsoo Han, Yifeng Liu, Simon Ginzinger, and
+		David Wishart. (2011) SHIFTX2: significantly improved protein chemical
+		shift
+		prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57.
+		doi: 10.1007/s10858-011-9478-4.
+	</longdescription>
+  <use>
+    <flag name="debug">Enables debug output in the shiftx2 java part</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
new file mode 100644
index 000000000..5a19e4b0b
--- /dev/null
+++ b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 java-pkg-simple python-r1 versionator
+
+MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))"
+MY_PATCH="20120106"
+MY_P="${PN}-v${MY_PV}-linux"
+
+DESCRIPTION="Predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins"
+HOMEPAGE="http://shiftx2.wishartlab.com/"
+SRC_URI="http://shiftx2.wishartlab.com/download/${MY_P}-${MY_PATCH}.tgz"
+
+SLOT="0"
+LICENSE="all-rights-reserved"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug"
+
+CDEPEND="dev-util/weka"
+
+RDEPEND="${CDEPEND}
+	dev-lang/R
+	sci-chemistry/reduce
+	>=virtual/jre-1.5"
+DEPEND="${CDEPEND}
+	>=virtual/jdk-1.5"
+
+S="${WORKDIR}"/${MY_P}
+
+QA_PREBUILT="/opt/.*"
+
+src_prepare() {
+	epatch "${FILESDIR}/gentoo-fixes.patch"
+	rm "${S}"/src/FeatureRanges.java || die
+
+	shared=$(echo "/usr/share/${PN}" | sed -e 's/\//\\\//g')
+	sed -i -e "s/PUT_GENTOO_SHARE_PATH_HERE/${shared}/g" "${S}/src/ShiftXp.java" || die
+
+	if use debug; then
+		sed -i -e 's/DEBUG = false/DEBUG = true/g' "${S}/src/ShiftXp.java" || die
+	fi
+
+	# hack alert!
+	sed \
+		-e '/-o/s:$(GCC):$(GCC) $(LDFLAGS):g' \
+		-e '/-o/s:$(CC):$(CC) $(LDFLAGS):g' \
+		-i modules/*/Makefile || die
+
+	sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
+}
+
+src_compile() {
+	mkdir "${S}"/build || die
+	ejavac -classpath "$(java-pkg_getjars weka)" -nowarn \
+		-d "${S}"/build $(find src/ -name "*.java")
+	jar cf "${PN}.jar" -C "${S}"/build . || die
+
+	einfo "Building module angles"
+	cd "${S}"/modules/angles || die
+	emake clean
+	emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" get_angles phipsi
+
+	einfo "Building module resmf"
+	cd "${S}"/modules/resmf || die
+	emake clean
+	emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" resmf
+
+	einfo "Building module effects"
+	cd "${S}"/modules/effects || die
+	emake clean
+	emake CFLAGS="${CFLAGS}" CC=$(tc-getCC) LINK="${LDFLAGS}" all
+}
+
+src_install() {
+	java-pkg_dojar "${PN}.jar"
+	java-pkg_dolauncher ${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin"
+
+	insinto /usr/share/${PN}
+	doins "${S}"/lib/{limitedcshift.dat,RandomCoil.csv,data-header.arff}
+	doins -r "${S}"/lib/predmodels
+
+	insinto /usr/share/${PN}/vader
+	doins -r "${S}"/modules/resmf/lib/*
+
+	local instdir="/opt/${PN}"
+	dodoc README 1UBQ.pdb
+	python_parallel_foreach_impl python_doscript "${S}"/*py
+
+	# other modules
+	dobin \
+		"${S}"/modules/angles/{get_angles,phipsi} \
+		"${S}"/modules/resmf/resmf \
+		"${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
+	exeinto ${instdir}/shifty3
+	doexe "${S}"/shifty3/xalign_x
+	dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x
+}