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-rw-r--r--academic/ugene/README1
-rw-r--r--academic/ugene/hmmer3.patch64
-rw-r--r--academic/ugene/slack-desc2
-rw-r--r--academic/ugene/ugene.SlackBuild12
-rw-r--r--academic/ugene/ugene.info6
5 files changed, 10 insertions, 75 deletions
diff --git a/academic/ugene/README b/academic/ugene/README
index 5ed2a5eaa6..ef532fe350 100644
--- a/academic/ugene/README
+++ b/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)
diff --git a/academic/ugene/hmmer3.patch b/academic/ugene/hmmer3.patch
deleted file mode 100644
index 9a91c068a2..0000000000
--- a/academic/ugene/hmmer3.patch
+++ /dev/null
@@ -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;
-
diff --git a/academic/ugene/slack-desc b/academic/ugene/slack-desc
index 7f8cef8e87..ea65c2afb7 100644
--- a/academic/ugene/slack-desc
+++ b/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
diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild
index 1013d5583b..4f54d0fc20 100644
--- a/academic/ugene/ugene.SlackBuild
+++ b/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
diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info
index 0f66ab8ead..99dde3d082 100644
--- a/academic/ugene/ugene.info
+++ b/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"
generated by cgit v1.2.3 (git 2.26.2) at 2024-12-28 07:12:31 +0000