Commit 1e21f696 authored by Rayan  CHIKHI's avatar Rayan CHIKHI
Browse files

fixing some mistakes

parent 1bac8ece
...@@ -23,15 +23,19 @@ def process_file(accession, region): ...@@ -23,15 +23,19 @@ def process_file(accession, region):
print("region - " + region) print("region - " + region)
startTime = datetime.now() startTime = datetime.now()
os.system(' '.join(["df", "-T"]))
os.system(' '.join(["cat","/dfT.txt"]))
os.system(' '.join(["lsblk"]))
os.system(' '.join(["cat","/lsblk.txt"]))
# go to /tmp (that's where local storage / nvme is) # go to /tmp (that's where local storage / nvme is)
# go to /data instead (EBS) # go to /data instead (EBS)
os.chdir("/mnt/serratus-data") os.chdir("/mnt/serratus-data")
os.system(' '.join(["pwd"])) os.system(' '.join(["pwd"]))
# check free space # check free space
os.system(' '.join(["df", "-T"]))
os.system(' '.join(["df", "-h","."])) os.system(' '.join(["df", "-h","."]))
os.system(' '.join(["lsblk"]))
# download reads from accession # download reads from accession
os.system('mkdir -p out/') os.system('mkdir -p out/')
......
...@@ -112,13 +112,13 @@ Resources: ...@@ -112,13 +112,13 @@ Resources:
Vcpus: 4 Vcpus: 4
Memory: 8000 # seems that 4000 wasn't enough for parallel-fastq-dump, 4 threads Memory: 8000 # seems that 4000 wasn't enough for parallel-fastq-dump, 4 threads
MountPoints: MountPoints:
- ContainerPath: "/serratus-data" - ContainerPath: "/mnt/serratus-data"
ReadOnly: false ReadOnly: false
SourceVolume: serratus-data SourceVolume: serratus-data
Volumes: Volumes:
- Name: serratus-data - Name: serratus-data
Host: Host:
SourcePath: "/serratus-data" SourcePath: "/mnt/serratus-data"
RetryStrategy: RetryStrategy:
Attempts: 1 Attempts: 1
RayanSerratusDlBatchProcessingJobQueue: RayanSerratusDlBatchProcessingJobQueue:
...@@ -182,7 +182,9 @@ Resources: ...@@ -182,7 +182,9 @@ Resources:
mkdir /mnt/serratus-data mkdir /mnt/serratus-data
echo -e "/dev/xvdh\t/mnt/serratus-data\text4\tdefaults\t0\t0" >> /etc/fstab echo -e "/dev/xvdh\t/mnt/serratus-data\text4\tdefaults\t0\t0" >> /etc/fstab
mount -a mount -a
chmod 777 /serratus-data lsblk > /lsblk.txt
df -T > /dfT.txt
chmod 777 /mnt/serratus-data
service docker restart service docker restart
--==MYBOUNDARY==-- --==MYBOUNDARY==--
......
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