diff --git a/Dockerfile b/Dockerfile index ef26ef2..89ee918 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:18.04 as builder +FROM ubuntu:20.04 as builder RUN apt-get update && \ apt-get upgrade -y && \ @@ -90,7 +90,12 @@ RUN wget https://github.com/samtools/samtools/archive/0.1.17.tar.gz && \ RUN SAMTOOLS="/tmp/samtools-0.1.17" cpanm --force -i Bio::DB::Sam@1.35 && chown -R root:root /usr/local/.cpanm -FROM ubuntu:18.04 +FROM ubuntu:20.04 + +RUN apt-get update && \ + apt-get upgrade -y && \ + apt-get install -y libncursesw5 && \ + rm -r /var/lib/apt/lists/* COPY --from=builder /opt/conda/bin/gfClient /opt/conda/bin/gfClient COPY --from=builder /opt/conda/bin/gfServer /opt/conda/bin/gfServer diff --git a/src/scripts/Cicero.sh b/src/scripts/Cicero.sh index 6a57470..91bc88c 100755 --- a/src/scripts/Cicero.sh +++ b/src/scripts/Cicero.sh @@ -334,10 +334,12 @@ parallel --joblog 02_Cicero.log $PARALLEL_ARG < cmds-02.sh ######################### echo "Step 03 - $(date +'%Y.%m.%d %H:%M:%S') - Combine" { -find $CICERO_DATADIR/$SAMPLE/*/ -type f -name 'unfiltered.fusion.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.fusion.txt -find $CICERO_DATADIR/$SAMPLE/*/ -type f -name 'unfiltered.internal.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.internal.txt +find $CICERO_DATADIR/$SAMPLE/ -mindepth 2 -type f -name 'unfiltered.fusion.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.fusion.txt +find $CICERO_DATADIR/$SAMPLE/ -mindepth 2 -type f -name 'unfiltered.internal.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.internal.txt } 1> 03_Combine.out 2> 03_Combine.err +wait + ## QC if [ ! -s $CICERO_DATADIR/$SAMPLE/unfiltered.fusion.txt ] then