some updates

Clairvoyante_1.0_ubuntu.2.def

+Bootstrap: docker
+From: ubuntu:latest
+
+%labels
+Maintainer by Emanuel Schmid @ VITAL-IT
+Version v1
+
+%help
+	
+%post
+
+# install software
+apt-get update -y -q && apt-get install -y -q \
+	build-essential \
+        gcc-multilib \
+        libboost-all-dev \
+        libhdf5-serial-dev \
+        zlib1g-dev \
+        pkg-config \
+        wget \
+	rsync \
+	unzip \
+	curl \
+	git-core \
+	python2.7 \
+	python-pip \
+	bzip2 
+
+cd /usr/local/
+git clone --depth=1 https://github.com/aquaskyline/Clairvoyante.git
+cd Clairvoyante
+curl http://www.bio8.cs.hku.hk/trainedModels.tbz | tar -jxf -
+
+pip install tensorflow
+pip install blosc
+pip install intervaltree
+pip install numpy
+
+
+%environment
+export LD_LIBRARY_PATH=/usr/local/miniconda/lib/:${LD_LIBRARY_PATH}
+export PATH=/usr/local/miniconda/bin/:/bin/${PATH}
+export PYTHONPATH=/usr/local/miniconda/lib/python2.7/site-packages
+
+%runscript
+exec /bin/bash "$@"

Clairvoyante_1.0_ubuntu.def

+Bootstrap: docker
+From: ubuntu:latest
+
+%labels
+Maintainer by Emanuel Schmid @ VITAL-IT
+Version v1
+
+%help
+	
+%post
+
+# install software
+apt-get update -y -q && apt-get install -y -q \
+	build-essential \
+        gcc-multilib \
+        libboost-all-dev \
+        libhdf5-serial-dev \
+        zlib1g-dev \
+        pkg-config \
+        wget \
+	rsync \
+	unzip \
+	bzip2 
+PREFIX=/usr/local/miniconda
+wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh --no-check-certificate
+bash miniconda.sh -b -p $PREFIX
+export PATH="$PREFIX/bin/:$PATH"
+conda config --add channels conda-forge
+conda config --add channels defaults
+conda config --add channels bioconda
+conda install -y -c bioconda clairvoyante
+conda remove tensorflow
+conda install tensorflow-gpu
+
+%environment
+export LD_LIBRARY_PATH=/usr/local/miniconda/lib/:${LD_LIBRARY_PATH}
+export PATH=/usr/local/miniconda/bin/:/bin/${PATH}
+export PYTHONPATH=/usr/local/miniconda/lib/python2.7/site-packages
+
+%runscript
+exec /bin/bash "$@"

PacBioSuiteV6.def

+Bootstrap: docker
+From: centos:latest
+
+%labels
+Maintainer by Emanuel Schmid @ VITAL-IT
+Version v6.0.0.47841
+
+%help
+Welcome to the smrtlink v510.26412 installation!
+This is the current PacBio collection of tools as in smrtlink version V5.1.0 from
+[I am link](https://www.pacb.com/support/software-downloads/).
+It furthermore includes the
+ - isoseq3
+ - FALCON (to do)
+Please invoke PB tools using "singularity exec --bind $PWD thisImage.img myCommand"
+valid ones are e.g.: blasr,quiver,pbalign,isoseq3,....
+
+%setup
+cp smrtlink_6.0.0.47841.zip $SINGULARITY_ROOTFS
+	
+%post
+
+# install software
+yum update -y -q && yum install -y -q \
+	build-essential \
+        gcc-multilib \
+        libboost-all-dev \
+        libhdf5-serial-dev \
+        zlib1g-dev \
+        pkg-config \
+        wget \
+	rsync \
+	unzip \
+	which \
+	bzip2 \
+	dirname
+    
+
+
+echo "add new user if not existent"
+	
+SMRT_USER=smrtanalysis
+if ! grep -c "smrtanalysis:" /etc/passwd
+then
+	useradd  -g users -d /home/$SMRT_USER -s /bin/bash -p PacBio $SMRT_USER
+else
+	echo 	"user already exists"
+fi
+
+echo "generate a new PacBio root directory and make smrtuser owner"
+
+SMRT=/opt/pacbio
+if [ ! -d $SMRT ]
+then
+	mkdir $SMRT
+	mv smrtlink_6.0.0.47841.zip $SMRT/
+	chown smrtanalysis:users $SMRT
+fi
+
+
+
+
+
+echo "now switch to smrt-user"
+
+su $SMRT_USER
+SMRT="/opt/pacbio"
+SMRT_ROOT="$SMRT/smrtlink"
+cd $SMRT
+
+echo "extract smrtlink"
+unzip smrtlink_6.0.0.47841.zip 
+
+if [ -d $SMRT_ROOT ] 
+then 
+	rm -rf $SMRT_ROOT
+	./smrtlink_6.0.0.47841.run --rootdir $SMRT_ROOT --smrttools-only	
+else
+	./smrtlink_6.0.0.47841.run --rootdir $SMRT_ROOT --smrttools-only	
+fi
+
+#wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda3.sh 
+#bash miniconda3.sh -b -p /opt/pacbio/miniconda
+#export PATH="/opt/pacbio/miniconda/bin/:$PATH"
+#conda config --add channels conda-forge
+#conda config --add channels defaults
+#conda config --add channels r
+#conda config --add channels bioconda
+#conda install -y isoseq3
+
+echo "cleaning up"
+#rm smrtlink_6.0.0.47841.*
+
+
+%environment
+export PATH=/opt/pacbio/smrtlink/smrtcmds/bin/:$PATH
+#export PATH=/opt/pacbio/miniconda/bin/:$PATH
+
+%runscript
+exec /bin/bash "$@"

gnommon.def

@@ -22,13 +22,15 @@ apt-get install -y unzip wget \
    
 cd /usr/local/
 wget -c ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--21_0_0.zip
+if [ ! -d ncbi/ncbi_cxx--21_0_0 ]
+then
 unzip -o ncbi_cxx--21_0_0.zip -d ncbi
 cd ncbi
 cd ncbi_cxx--21_0_0/
-./configure --without-gui --without-internal
+./configure --without-gui --with-mt 
 cd GCC700-DebugMT64/build
 make all_r
-
+fi
 
 %environment
 export PATH=/usr/local/ncbi/ncbi_cxx--21_0_0/GCC700-DebugMT64/bin/:$PATH

pbmm2.def

@@ -3,7 +3,7 @@ From: centos:latest
 
 %labels
 Maintainer by Emanuel Schmid @ VITAL-IT
-Version v0.5.1
+Version v0.9
 
 %help
 This is the current PacBio minimap-->quiver program pbmm2
@@ -35,7 +35,7 @@ conda config --add channels conda-forge
 conda config --add channels defaults
 conda config --add channels r
 conda config --add channels bioconda
-conda install -y pbmm2
+conda install -y pbmm2=0.9.0
 
 %environment
 export PATH=/opt/pacbio/miniconda/bin/:$PATH