academic/ugene: Updated for version 1.25.0.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

academic/ugene/README

@@ -48,6 +48,7 @@ program. All of them are available at SlackBuilds.org:
 - cufflinks (A reference-guided assembler for RNA-Seq experiments)
 - cutadapt (Trim adapters from high-throughput sequencing reads)
 - fastqc (A quality control tool for high throughput sequence data)
+- HMMER (Biosequence analysis using profile hidden Markov models)
 - ncbi-blast (BLAST: Basic Local Alignment Search Tool)
 - ncbi-blast-plus (BLAST+ Command Line Applications)
 - PhyML (Phylogenetic estimation using Maximum Likelihood)

academic/ugene/hmmer3.patch

@@ -1,64 +0,0 @@
-diff --git a/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp b/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp
-index b458c12..23fa49b 100644
---- a/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp
-+++ b/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp
-@@ -33,7 +33,7 @@ float infinity() {
- }
- 
- bool isfin( float x ) {
--    return !isnan( x ) && !isinf( x );
-+    return !std::isnan( x ) && !std::isinf( x );
- }
- 
- const char TERM_SYM = '\0';
-diff --git a/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp b/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp
-index 9050f1c..6032970 100644
---- a/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp
-+++ b/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp
-@@ -134,7 +134,7 @@ p7_Decoding(const P7_OPROFILE *om, const P7_OMX *oxf, P7_OMX *oxb, P7_OMX *pp)
-         if (oxb->has_own_scales) scaleproduct *= oxf->xmx[i*p7X_NXCELLS+p7X_SCALE] /  oxb->xmx[i*p7X_NXCELLS+p7X_SCALE];
-     }
- 
--    if (isinf(scaleproduct)) return eslERANGE;
-+    if (std::isinf(scaleproduct)) return eslERANGE;
-     else                     return eslOK;
- }
- 
-@@ -188,7 +188,7 @@ p7_DomainDecoding(const P7_OPROFILE *om, const P7_OMX *oxf, const P7_OMX *oxb, P
-     }
-     ddef->L = oxf->L;
- 
--    if (isinf(scaleproduct)) return eslERANGE;
-+    if (std::isinf(scaleproduct)) return eslERANGE;
-     else                     return eslOK;
- }
- /*------------------ end, posterior decoding --------------------*/
-diff --git a/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/fwdback.cpp b/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/fwdback.cpp
-index 5bafaa4..413a6fe 100644
---- a/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/fwdback.cpp
-+++ b/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/fwdback.cpp
-@@ -465,9 +465,9 @@ forward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7
-     /* On an underflow (which shouldn't happen), we counterintuitively return infinity:
-     * the effect of this is to force the caller to rescore us with full range.
-     */
--    if       (isnan(xC))      ESL_EXCEPTION(eslERANGE, "forward score is NaN");
-+    if       (std::isnan(xC))      ESL_EXCEPTION(eslERANGE, "forward score is NaN");
-     else if  (L>0 && xC == 0.0)      ESL_EXCEPTION(eslERANGE, "forward score underflow (is 0.0)");
--    else if  (isinf(xC) == 1) ESL_EXCEPTION(eslERANGE, "forward score overflow (is infinity)");
-+    else if  (std::isinf(xC) == 1) ESL_EXCEPTION(eslERANGE, "forward score overflow (is infinity)");
- 
-     if (opt_sc != NULL) *opt_sc = ox->totscale + log((double)(xC * om->xf[p7O_C][p7O_MOVE]));
-     return eslOK;
-@@ -742,9 +742,9 @@ backward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, c
-     if (bck->debugging) p7_omx_DumpFBRow(bck, TRUE, 0, 9, 4, bck->xmx[p7X_E], bck->xmx[p7X_N],  bck->xmx[p7X_J], bck->xmx[p7X_B],  bck->xmx[p7X_C]);	/* logify=TRUE, <rowi>=0, width=9, precision=4*/
- #endif
- 
--    if       (isnan(xN))      ESL_EXCEPTION(eslERANGE, "backward score is NaN");
-+    if       (std::isnan(xN))      ESL_EXCEPTION(eslERANGE, "backward score is NaN");
-     else if  (L>0 && xN == 0.0)      ESL_EXCEPTION(eslERANGE, "backward score underflow (is 0.0)");
--    else if  (isinf(xN) == 1) ESL_EXCEPTION(eslERANGE, "backward score overflow (is infinity)");
-+    else if  (std::isinf(xN) == 1) ESL_EXCEPTION(eslERANGE, "backward score overflow (is infinity)");
- 
-     if (opt_sc != NULL) *opt_sc = bck->totscale + log((double)xN);
-     return eslOK;
-

academic/ugene/slack-desc

@@ -16,4 +16,4 @@ ugene: user nterface. The toolkit supports multiple biological data formats
 ugene: and allows the retrieval of data from remote data sources.
 ugene:
 ugene: Home: http://ugene.net/
-ugene: References: /usr/doc/ugene-1.22.0/References
+ugene: References: /usr/doc/ugene-1.25.0/References

academic/ugene/ugene.SlackBuild

@@ -23,13 +23,13 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=ugene
-VERSION=${VERSION:-1.22.0}
+VERSION=${VERSION:-1.25.0}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
-    i?86) ARCH=i486 ;;
+    i?86) ARCH=i586 ;;
     arm*) ARCH=arm ;;
        *) ARCH=$( uname -m ) ;;
   esac
@@ -40,8 +40,8 @@ TMP=${TMP:-/tmp/SBo}
 PKG=$TMP/package-$PRGNAM
 OUTPUT=${OUTPUT:-/tmp}
 
-if [ "$ARCH" = "i486" ]; then
-  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
   LIBDIRSUFFIX=""
   QMAKECONFIG=""
 elif [ "$ARCH" = "i686" ]; then
@@ -77,8 +77,6 @@ find -L . \
 sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri
 sed -i "s:/share/man:/man:g" src/ugene_globals.pri
 
-patch -p1 < $CWD/hmmer3.patch
-
 qmake-qt5 $QMAKECONFIG -r \
 QMAKE_CFLAGS="$SLKCFLAGS" \
 QMAKE_CXXFLAGS="$SLKCFLAGS"
@@ -90,7 +88,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  build.txt COPYRIGHT LICENSE LICENSE.3rd_party \
+  build.txt COPYRIGHT LICENSE.txt LICENSE.3rd_party.txt \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 

academic/ugene/ugene.info

@@ -1,8 +1,8 @@
 PRGNAM="ugene"
-VERSION="1.22.0"
+VERSION="1.25.0"
 HOMEPAGE="http://ugene.net/"
-DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/ugene/ugene-1.22.0.tar.gz"
-MD5SUM="c876d46c75628a96ee1be5ae86b33b9c"
+DOWNLOAD="http://ugene.net/downloads/ugene-1.25.0.tar.gz"
+MD5SUM="0e4ab44ca7842aa7392e92e417881dd2"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="qt5-webkit"