Command not found in docker image
I am trying to run this command on LSF cluster using docker image. However, I keep getting the error below. Can someone please help me figure out the issue?
Command:
export CUR_STEP="/usr/local/bbmap/demuxbyname.sh";
export java="/usr/local/openjdk-8/bin/java"
MEM=100;
export sortedFQ="${BASE}/WXS_Aquilla/01-RAW/${PR}/${FULLSM}/paire_test_sorted.fastq";
export column=2;
export DELIM=":";
export COLNUM=2;
export sampleFQ="${BASE}/WXS_Aquilla/01-RAW/${PR}/${FULLSM}/ADNI_1380"
bsub
-J "${FULLSM}_bbduk_demulti"
-o "${BASE}/WXS_Aquilla/01-RAW/${PR}/${FULLSM}/${FULLSM}.${BAMBASE}_bbduk_demulti.%J"
-u "${EMAIL}"
-n1 -W 1440
-R "rusage[mem=120192]"
-q research-hpc
-a 'docker(achalneupane/bbduk:latest)'
entrypoint.sh;
Error:
Status: Downloaded newer image for achalneupane/bbduk:latest
[20201106_025413] /usr/local/bbmap/demuxbyname.sh starting
java -ea -Xmx100g -Xms100g -cp /usr/local/bbmap/current/ jgi.DemuxByName2 -Xmx100g in=/gscmnt/gc2645/wgs/WXS_Aquilla/01-RAW/ADNI_WGS/ADNI_1380^LP6005117-DNA_G04^ADNI_WGS/paire_test_sorted.fastq delimiter=: column=2 out=/gscmnt/gc2645/wgs/WXS_Aquilla/01-RAW/ADNI_WGS/ADNI_1380^LP6005117-DNA_G04^ADNI_WGS/ADNI_1380%_#.fq
/usr/local/bbmap/demuxbyname.sh: line 149: java: command not found
Command exited with non-zero status 127
Command being timed: "/usr/local/bbmap/demuxbyname.sh -Xmx100g in=/gscmnt/gc2645/wgs/WXS_Aquilla/01-RAW/ADNI_WGS/ADNI_1380^LP6005117-DNA_G04^ADNI_WGS/paire_test_sorted.fastq delimiter=: column=2 out=/gscmnt/gc2645/wgs/WXS_Aquilla/01-RAW/ADNI_WGS/ADNI_1380^LP6005117-DNA_G04^ADNI_WGS/ADNI_1380%_#.fq"
My docker file looks like this:
FROM openjdk:8-jre
LABEL maintainer="AN <[email protected]>"
LABEL org.label-schema.schema-version="1.0"
# LABEL org.label-schema.build-date=$BUILD_DATE
LABEL org.label-schema.name="XXX/bbduk"
LABEL org.label-schema.description="Image for creating interleaved fastq"
ENV BBMAP_VERSION 38.87
ENV BBMAP_DIR /usr/local/bbmap
WORKDIR /tmp
RUN apt-get update -y
&& apt-get install --no-install-recommends -y
make
gcc
g++
libz-dev
libbz2-dev
liblzma-dev
ncurses-dev
bc
libnss-sss
time
WORKDIR /usr/local
RUN set -eux;
wget -O bbmap.tar.gz https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VERSION}.tar.gz/download
&& tar -zxf bbmap.tar.gz
&& rm bbmap.tar.gz
COPY ./entrypoint.sh /usr/local/bin/
ENV PATH ${BBMAP_DIR}:${PATH}
## Add ENV for Shell scripts from BBMAP
ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
# CMD ["/bin/bash"]
Entrypoint.sh
"${CUR_STEP}" -Xmx${MEM}g in=${sortedFQ} delimiter=${DELIM} column=${COLNUM} out=${sampleFQ}%_#.fq
Source: Docker Questions