enforce pysam 0.10 and htslib 1.3 temporarily

install-CGAT-tools.sh

@@ -328,7 +328,7 @@ if [[ "$OS" != "travis" ]] ; then
 
       # SLV: workaround to
       # https://github.com/conda/conda/issues/4955
-      conda install -f htslib=1.3 --override-channels --channel conda-forge --channel defaults --channel r --channel bioconda --yes
+      conda install -f pysam=0.10 htslib=1.3 --override-channels --channel conda-forge --channel defaults --channel r --channel bioconda --yes
 
       # Set up other environment variables
       setup_env_vars
@@ -412,7 +412,7 @@ if [[ $TRAVIS_INSTALL ]] || [[ $JENKINS_INSTALL ]] ; then
 
    # SLV: workaround to
    # https://github.com/conda/conda/issues/4955
-   conda install -f htslib=1.3 --override-channels --channel conda-forge --channel defaults --channel r --channel bioconda --yes
+   conda install -f pysam=0.10 htslib=1.3 --override-channels --channel conda-forge --channel defaults --channel r --channel bioconda --yes
 
 
    # python preparation
@@ -746,17 +746,22 @@ do
 done # while-loop
 
 # sanity checks
-if [[ $INSTALL_SCRIPTS ]] && [[ $INSTALL_DEVEL ]] ; then
-
-   echo
-   echo " Incorrect input arguments: mixing --cgat-scripts and --cgat-devel is not permitted."
-   echo " Installation aborted. Please run -h option."
-   echo
-   exit 1
-
+if [[ ! $TRAVIS_INSTALL ]] && [[ ! $JENKINS_INSTALL ]] ; then
+    if [[ $INSTALL_SCRIPTS ]] && [[ $INSTALL_DEVEL ]] ; then
+       echo
+       echo " Incorrect input arguments: mixing --cgat-scripts and --cgat-devel is not permitted."
+       echo " Installation aborted. Please run -h option."
+       echo
+       exit 1
+    elif [[ ! $INSTALL_SCRIPTS  ]] && [[ ! $INSTALL_DEVEL ]] ; then
+       echo
+       echo " Error: you need to either specify --cgat-scripts or --cgat-devel."
+       echo " Installation aborted. Please run -h option."
+       echo
+       exit 1
+    fi
 fi
 
-
 # perform actions according to the input parameters processed
 if [[ $TRAVIS_INSTALL ]] ; then