From 0bb3efdbaef7cd37a93473093ea666cb10ff832d Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 27 Nov 2016 00:09:09 +0000 Subject: academic/ugene: Updated for version 1.25.0. Signed-off-by: David Spencer --- academic/ugene/README | 1 + academic/ugene/hmmer3.patch | 64 ----------------------------------------- academic/ugene/slack-desc | 2 +- academic/ugene/ugene.SlackBuild | 12 ++++---- academic/ugene/ugene.info | 6 ++-- 5 files changed, 10 insertions(+), 75 deletions(-) delete mode 100644 academic/ugene/hmmer3.patch (limited to 'academic/ugene') 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, =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" -- cgit v1.2.3