Commit 5ebe3309 authored by Rayan's avatar Rayan
Browse files

attempt to download missing files

parent 85d5f0b9
......@@ -19,7 +19,7 @@ ARG AWS_SECRET_ACCESS_KEY
#ENV AWS_SECRET_ACCESS_KEY=$AWS_SECRET_ACCESS_KEY
#SRA toolkit (from serratus-dl)
ENV SRATOOLKITVERSION='2.10.4'
ENV SRATOOLKITVERSION='2.10.7'
RUN wget --quiet https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRATOOLKITVERSION}/sratoolkit.${SRATOOLKITVERSION}-centos_linux64.tar.gz &&\
tar xzf sratoolkit.${SRATOOLKITVERSION}-centos_linux64.tar.gz &&\
rm -f sratoolkit.${SRATOOLKITVERSION}-centos_linux64.tar.gz &&\
......@@ -45,6 +45,8 @@ RUN chmod +x parallel-fastq-dump
RUN wget --quiet http://opengene.org/fastp/fastp
RUN chmod +x fastp
RUN mkdir -p /mnt/serratus-data # for local testing
RUN pwd
RUN df -T
RUN ls
......
......@@ -80,7 +80,7 @@ def process_file(accession, region):
# 'is larger than maximum allowed: skipped' solved by:
# https://wiki.rc.hms.harvard.edu/display/O2/Aspera+to+download+NCBI+SRA+data
#os.system('prefetch --max-size 35G '+accession)
os.system('prefetch '+accession)
os.system('prefetch --max-size 35G '+accession)
prefetch_time = datetime.now() - prefetch_start
sdb_log(sdb,accession,'prefetch_time',int(prefetch_time.seconds))
os.system('mkdir -p tmp/')
......
File mode changed from 100644 to 100755
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