academic/vCAPS_coevolution: Removed (ftb + no active maintainer).

Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>

6 files changed, 0 insertions, 315 deletions

diff --git a/academic/vCAPS_coevolution/README b/academic/vCAPS_coevolution/README
deleted file mode 100644
index 27ebb623a0..0000000000
--- a/academic/vCAPS_coevolution/README
+++ /dev/null
@@ -1,32 +0,0 @@
-vCAPS: (verbose) Coevolution Analysis using Protein Sequences
-
-CAPS is aimed at measuring the coevolution between amino acid sites
-belonging to the same protein (intra-molecular coevolution) or to two
-functionally or physically interacting proteins (inter-molecular
-coevolution). The Software implements an improved method to detect
-intra-molecular coevolution as published in Genetics (Fares and Travers,
-2006) and also inter-protein coevolution analysis. The improved scoring
-of amino acid sites is obtained by maximum likelihood ancestral state
-reconstruction along with simulations to assess significance.
-
-In addition, a test which assesses whether two proteins are interacting
-is implemented.
-
-NOTE:
-This applies an _unofficial_ patch to enable more verbose output of the
-program, including CAPS generated phylogenetic trees and p-values of the
-pairwise results. The produced executable is called "vCAPS" and can be
-installed along "caps" from CAPS_coevolution. Building CAPS from source
-requires the Bio++ 1.9 suite, also available at SBo, which can be safely
-installed along the current version. Fore details of the patch see pre-
-print at bioRxiv by Petrov et al.:
-https://doi.org/10.1101/2020.09.29.315374
-
-CITING:
-CAPS: coevolution analysis using protein sequences. Fares MA, McNally D.
-Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535
-
-The mathematical model has been described separately:
-A novel method for detecting intramolecular coevolution: adding a
-further dimension to selective constraints analyses. Fares MA, Travers
-SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113
diff --git a/academic/vCAPS_coevolution/References b/academic/vCAPS_coevolution/References
deleted file mode 100644
index e8236cd282..0000000000
--- a/academic/vCAPS_coevolution/References
+++ /dev/null
@@ -1,14 +0,0 @@
-If you use CAPS in your research, please include the following citations:
-
-CAPS: coevolution analysis using protein sequences.
-Fares MA, McNally D.
-Bioinformatics. 2006 Nov 15;22(22):2821-2.
-PMID: 17005535
-https://www.ncbi.nlm.nih.gov/pubmed/17005535
-
-The mathematical model has been described separately:
-A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.
-Fares MA, Travers SA.
-Genetics. 2006 May;173(1):9-23.
-PMID: 16547113
-https://www.ncbi.nlm.nih.gov/pubmed/16547113
diff --git a/academic/vCAPS_coevolution/caps_verbose.patch b/academic/vCAPS_coevolution/caps_verbose.patch
deleted file mode 100644
index 7f64d80f34..0000000000
--- a/academic/vCAPS_coevolution/caps_verbose.patch
+++ /dev/null
@@ -1,114 +0,0 @@
-diff -pruN orig/caps.cpp new/caps.cpp
---- orig/caps.cpp	2012-12-15 17:13:23.000000000 +0200
-+++ new/caps.cpp	2020-09-09 23:07:46.080566000 +0300
-@@ -14,7 +14,7 @@
- #include <gsl/gsl_statistics.h>
- #include<sys/time.h>
- #include<iomanip>
--
-+#include <bits/stdc++.h> 
- 
- 
- 
-@@ -69,6 +69,8 @@
- const gsl_rng_type * T;
- gsl_rng *r;
- 
-+vector<double> totaltempnew;
-+double alphathresh = 0;
- int main(int argc, char *argv[]){
- 
- 
-@@ -543,16 +545,27 @@ int main(int argc, char *argv[]){
- 
- 
- 					print_splash(output);
-+					OUTPUT << "\n\File1: " << files[i] << endl;
- 					vec1.print_to_fasta(output.c_str());
-+					OUTPUT << "\n\nFile2: " << files[j] << endl;
- 					vec2.print_to_fasta(output.c_str());
- 					int length1 = vec1.sequences[0].length();			
- 					int length2 = vec2.sequences[0].length();
- 
-+					OUTPUT << "\n\nLength1: " << length1 << endl;
-+					OUTPUT << "Length2: " << length2 << endl;
- 
- 
- 					if(tree_in ==0){
- 						tree1 = create_input_tree(vec1.names, vec1.sequences);
- 						tree2 = create_input_tree(vec2.names, vec2.sequences);
-+						
-+						// Output the CAPS generated trees to the .out file of each pair
-+						string temptre1 = TreeTemplateTools::treeToParenthesis(*tree1, true);
-+						string temptre2 = TreeTemplateTools::treeToParenthesis(*tree2, true);
-+						OUTPUT << "\n" << endl;
-+						OUTPUT << "CAPS generated tree 1: " << temptre1 << endl;
-+						OUTPUT << "CAPS generated tree 2: " << temptre2 << endl;
- 					}/*else if(tree_in ==1 && variable==1){
- 
- 					   std::auto_ptr<DistanceMatrix> DS;
-@@ -666,6 +679,7 @@ int main(int argc, char *argv[]){
- 					int value = floor(((totaltemp.size())*(1-(threshval))))+1;
- 
- 					threshold = totaltemp[value];
-+					totaltempnew = totaltemp;
- 
- 
- 					/*=======================================================*/
-@@ -870,6 +884,30 @@ int Chi_squared (int num_pairs, int num_
- 
- }		/* -----  end of function Chi_squared  ----- */
- 
-+/* 
-+ * ===  FUNCTION  ======================================================================
-+ *         Name:  find_alpha
-+ *  Description:  Find the index of an element in a vector totaltemp
-+ *    Help from:  https://www.geeksforgeeks.org/how-to-find-index-of-a-given-element-in-a-vector-in-cpp/
-+ *                https://stackoverflow.com/questions/8647635/elegant-way-to-find-closest-value-in-a-vector-from-above
-+ *       Author:  Petar Petrov, University of Turku (Finland); pebope@utu.fi
-+ * =====================================================================================
-+ */
-+double getIndex(std::vector<double> const& v, double K) 
-+{ 
-+    auto const it = std::lower_bound(v.begin(), v.end(), fabs(K));
-+    //auto it = std::upper_bound(v.begin(), v.end(), fabs(K));
-+  
-+    if (it != v.end()) { 
-+        int index = distance(v.begin(), it);
-+	alphathresh = (((int)1+(double)v.size()-(int)index)/(double)v.size());
-+	return alphathresh;
-+        //cerr << index << "\t" << alphathresh << endl; 
-+    } 
-+    else { 
-+        cerr << "ELEMENT NOT FOUND!" << endl; 
-+    } 
-+} 
- 
- 
- 
-@@ -890,9 +928,9 @@ int print_inter(vector<double>& Correl1,
- 	output << endl << endl;
- 
- 	output << "Coevolving Pairs of amino acid sites\n";
--	output << "=============================================================================\n";
--	output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\n\n";
--	output << "=============================================================================\n";
-+	output << "================================================================================================================================\n";
-+	output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\tP-value1\tP-value2\tMean P-value\tCorrelation1\tCorrelation2\n\n";
-+	output << "================================================================================================================================\n";
- 
- 	//double mean = average_vec<double>(Correl);
- 	//double SD = SD_vf(Correl, mean);
-@@ -951,9 +989,11 @@ int print_inter(vector<double>& Correl1,
- 
- 						//	}
- 
-+						double Alpha1 = getIndex(totaltempnew, Correl1[cor]);
-+						double Alpha2 = getIndex(totaltempnew, Correl2[cor]);
- 						//if(bootval>=bootcut && re1<=8 && re2<=8 ){
- 						if(bootval>=bootcut){
--							output << i+1 << "(" << i-gaps1+1 << ")\t\t" << j+1 << "(" << (j+1)-gaps2 << ")\t\t" << averDi << "\t\t" << averDj << "\t\t" << (Correl1[cor]+Correl2[cor])/2 << "\t" << bootval << endl; 
-+							output << i+1 << "(" << i-gaps1+1 << ")\t\t" << j+1 << "(" << (j+1)-gaps2 << ")\t\t" << averDi << "\t\t" << averDj << "\t" << (Correl1[cor]+Correl2[cor])/2 << "\t" << bootval << "\t" << Alpha1 << "\t" << Alpha2 << "\t" << (Alpha1+Alpha2)/2 << "\t" << Correl1[cor] << "\t" << Correl2[cor] << endl; 
- 							signif.push_back(((Correl1[cor]+Correl2[cor])/2));
- 							++pairs;
- 							vector<int> tem;
diff --git a/academic/vCAPS_coevolution/slack-desc b/academic/vCAPS_coevolution/slack-desc
deleted file mode 100644
index 5cd78f0770..0000000000
--- a/academic/vCAPS_coevolution/slack-desc
+++ /dev/null
@@ -1,19 +0,0 @@
-# HOW TO EDIT THIS FILE:
-# The "handy ruler" below makes it easier to edit a package description.
-# Line up the first '|' above the ':' following the base package name, and
-# the '|' on the right side marks the last column you can put a character in.
-# You must make exactly 11 lines for the formatting to be correct.  It's also
-# customary to leave one space after the ':' except on otherwise blank lines.
-
-                 |-----handy-ruler------------------------------------------------------|
-vCAPS_coevolution: vCAPS_coevolution (Coevolution Analysis using Protein Sequences)
-vCAPS_coevolution:
-vCAPS_coevolution: CAPS is aimed at measuring the coevolution between amino acid
-vCAPS_coevolution: sites belonging to the same protein (intra-molecular coevolution)
-vCAPS_coevolution: or to two functionally or physically interacting proteins (inter-
-vCAPS_coevolution: molecular coevolution). In addition, a test which assesses
-vCAPS_coevolution: whether two proteins are interacting is implemented.
-vCAPS_coevolution:
-vCAPS_coevolution: Home: http://bioinf.gen.tcd.ie/~faresm/software/software.html
-vCAPS_coevolution:
-vCAPS_coevolution:
diff --git a/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild b/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild
deleted file mode 100644
index 9b000762b1..0000000000
--- a/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild
+++ /dev/null
@@ -1,126 +0,0 @@
-#!/bin/bash
-
-# Slackware build script for vCAPS_coevolution
-
-# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com
-# All rights reserved.
-#
-# Redistribution and use of this script, with or without modification, is
-# permitted provided that the following conditions are met:
-#
-# 1. Redistributions of this script must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#
-#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
-#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
-#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-cd $(dirname $0) ; CWD=$(pwd)
-
-PRGNAM=vCAPS_coevolution
-VERSION=${VERSION:-2.0_1UN}
-BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}
-PKGTYPE=${PKGTYPE:-tgz}
-
-SRCNAM=caps
-SRCVER=2.0
-BINNAM=vCAPS
-
-if [ -z "$ARCH" ]; then
-  case "$( uname -m )" in
-    i?86) ARCH=i586 ;;
-    arm*) ARCH=arm ;;
-       *) ARCH=$( uname -m ) ;;
-  esac
-fi
-
-# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
-# the name of the created package would be, and then exit. This information
-# could be useful to other scripts.
-if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
-  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
-  exit 0
-fi
-
-TMP=${TMP:-/tmp/SBo}
-PKG=$TMP/package-$PRGNAM
-OUTPUT=${OUTPUT:-/tmp}
-
-if [ "$ARCH" = "i586" ]; then
-  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
-  LIBDIRSUFFIX=""
-elif [ "$ARCH" = "i686" ]; then
-  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
-  LIBDIRSUFFIX=""
-elif [ "$ARCH" = "x86_64" ]; then
-  SLKCFLAGS="-O2 -fPIC"
-  LIBDIRSUFFIX="64"
-else
-  SLKCFLAGS="-O2"
-  LIBDIRSUFFIX=""
-fi
-
-# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay!
-LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9"
-
-set -e
-
-rm -rf $PKG
-mkdir -p $TMP $PKG $OUTPUT
-cd $TMP
-rm -rf ${SRCNAM}${SRCVER}_src
-unzip $CWD/${SRCNAM}2_src.zip
-cd ${SRCNAM}${SRCVER}_src
-chown -R root:root .
-find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
-  -o -perm 511 \) -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
-
-# This is needed for gcc in Slackware 14.2
-sed -i "s:CC=g++ -g:CC=g++ -g -std=c++11:" Makefile
-
-# Use our CFLAGS and the custom (legacy) lib path
-sed -i "s:CFLAGS=:CFLAGS=$SLKCFLAGS $LIBDIRPATH:" Makefile
-
-# Find the legacy bpp libraries
-sed -i "s:-lbpp-phyl:-L/usr/lib${LIBDIRSUFFIX}/Bpp1.9 -lbpp-phyl:g" Makefile
-sed -i "s:-lbpp-numcalc:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-numcalc:g" Makefile
-sed -i "s:-lbpp-utils:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-utils:g" Makefile
-sed -i "s:-lbpp-seq:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-seq:g" Makefile
-
-# Rename the produced executable 
-sed -i "s:-o caps:-o $BINNAM:" Makefile
-
-# Use our unofficial patch
-patch -p1 -i $CWD/caps_verbose.patch
-
-make all
-
-# Install the binary produced from our patched source, as "vCAPS"
-install -D -m755 $BINNAM $PKG/usr/bin/$BINNAM
-
-mkdir -p $PKG/usr/share/$PRGNAM
-cp -a sample structures trees TLR1.fa.out $PKG/usr/share/$PRGNAM
-
-mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
-cp -a \
-  caps_manual.pdf \
-  $PKG/usr/doc/$PRGNAM-$VERSION
-cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
-cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
-
-mkdir -p $PKG/install
-cat $CWD/slack-desc > $PKG/install/slack-desc
-
-cd $PKG
-/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
diff --git a/academic/vCAPS_coevolution/vCAPS_coevolution.info b/academic/vCAPS_coevolution/vCAPS_coevolution.info
deleted file mode 100644
index 84ebd91d4c..0000000000
--- a/academic/vCAPS_coevolution/vCAPS_coevolution.info
+++ /dev/null
@@ -1,10 +0,0 @@
-PRGNAM="vCAPS_coevolution"
-VERSION="2.0_1UN"
-HOMEPAGE="http://bioinf.gen.tcd.ie/~faresm/software/software.html"
-DOWNLOAD="http://bioinf.gen.tcd.ie/~faresm/software/files/caps2_src.zip"
-MD5SUM="0914007c32ed22a9cb8a47b55cd18a39"
-DOWNLOAD_x86_64=""
-MD5SUM_x86_64=""
-REQUIRES="bpp1.9-phyl"
-MAINTAINER="Petar Petrov"
-EMAIL="slackalaxy@gmail.com"