Merge branch 'master' into ct-update-novoalign

ncbi.py

@@ -85,6 +85,7 @@ def tbl_transfer_common(cmap, ref_tbl, out_tbl, alt_chrlens, oob_clip=False):
                                 row[0] = '<1'
                             if row[1] == None:
                                 row[1] = '>{}'.format(alt_chrlens[altid])
+                            feature_keep = True
                         else:
                             feature_keep = False
                             continue
@@ -203,7 +204,7 @@ def tbl_transfer_prealigned(inputFasta, refFasta, refAnnotTblFiles, outputDir, o
             cmap = interhost.CoordMapper()
             cmap.load_alignments([combined_fasta_filename])
             # sequences in the fasta file here should NOT include gaps
-            # since alt_chrlens is only used to in the case of features that would 
+            # since alt_chrlens is only used in the case where features would 
             # extend beyond the genome (for reporting >{seq.len})
             alt_chrlens = {}#fasta_chrlens(combined_fasta_filename)
             alt_chrlens[seq.id] = len(seq.seq.ungap("-"))

requirements-conda.txt

@@ -1,7 +1,7 @@
 blast=2.6.0
 bmtagger=3.101
 bwa=0.7.15
-diamond=0.8.22=2
+diamond=0.8.36
 gatk=3.6
 kraken-all=0.10.6_eaf8fb68 # [linux]
 krona=2.7

tools/diamond.py

@@ -12,8 +12,8 @@
 import tools
 import util.file
 
-TOOL_VERSION = '0.8.22'
-CONDA_VERSION = tools.CondaPackageVersion('0.8.22', '2')
+TOOL_VERSION = '0.8.36'
+CONDA_VERSION = tools.CondaPackageVersion(TOOL_VERSION)
 
 log = logging.getLogger(__name__)
 

travis/install-conda.sh

@@ -46,7 +46,7 @@ else # if it does not exist, we need to install miniconda
     conda config --add channels conda-forge
     conda install -y -q conda=4.2 # pin to 4.2.* until this is fixed: https://github.com/conda/conda-build/issues/1666
     conda config --set auto_update_conda false
-    conda install -y java-jdk==8.0.92
+    conda install -y java-jdk==8.0.112
     conda install -y conda-build # needed to build recipe
     conda install -y anaconda-client # needed to upload build package to anaconda.org
     conda install -y -c conda-forge curl # the bioconda curl is broken as of 21 Feb 2017

travis/trigger-tests-in-other-repo.sh

@@ -2,15 +2,24 @@
 
 echo "Script called to trigger tests in external repository..."
 
-# only initiate tests in other repo if the travis token string has a value
-if [ ! -z "$TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO" ]; then
-    echo "TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO is defined"
-        # if this is a tagged release add that information to the dependent build request
-    if [ -n "$TRAVIS_TAG" ]; then
-        ./travis/trigger-travis.sh --script "travis_wait 75 env UPSTREAM_BRANCH=$TRAVIS_BRANCH UPSTREAM_TAG=$TRAVIS_TAG ./travis/tests-unit.sh" broadinstitute viral-ngs-deploy $TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO #"UPSTREAM_BRANCH=$TRAVIS_BRANCH UPSTREAM_TAG=$TRAVIS_TAG"
+# parse out the second part of the job number (the '1' of '223.1')
+JOB_NUMBER=$(echo $TRAVIS_JOB_NUMBER | perl -lape 's/^(\d+)\.(\d+)/$2/g')
+
+# if this is the first job in the matrix, only then trigger the external 
+# repository to avoid triple-building the Docker image
+if [ "$JOB_NUMBER" == "1" ]; then
+    # only initiate tests in other repo if the travis token string has a value
+    if [ ! -z "$TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO" ]; then
+        echo "TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO is defined. Triggering downstream repo..."
+            # if this is a tagged release add that information to the dependent build request
+        if [ -n "$TRAVIS_TAG" ]; then
+            ./travis/trigger-travis.sh --script "travis_wait 75 env UPSTREAM_BRANCH=$TRAVIS_BRANCH UPSTREAM_TAG=$TRAVIS_TAG ./travis/tests-unit.sh" broadinstitute viral-ngs-deploy $TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO #"UPSTREAM_BRANCH=$TRAVIS_BRANCH UPSTREAM_TAG=$TRAVIS_TAG"
+        else
+            ./travis/trigger-travis.sh --script "travis_wait 75 env UPSTREAM_BRANCH=$TRAVIS_BRANCH ./travis/tests-unit.sh" broadinstitute viral-ngs-deploy $TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO #"UPSTREAM_BRANCH=$TRAVIS_BRANCH"
+        fi
     else
-        ./travis/trigger-travis.sh --script "travis_wait 75 env UPSTREAM_BRANCH=$TRAVIS_BRANCH ./travis/tests-unit.sh" broadinstitute viral-ngs-deploy $TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO #"UPSTREAM_BRANCH=$TRAVIS_BRANCH"
+        echo "TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO is undefined. Check the secure variable."
     fi
 else
-    echo "TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO is undefined. Check the secure variable."
+    echo "Not triggering, this is not the first job in the upstream build matrix."
 fi