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GUDMAP_RBK
RNA-seq
Commits
b2b91ce9
Commit
b2b91ce9
authored
4 years ago
by
Gervaise Henry
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Update bagit to bag in createTestData
parent
5a7daad9
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!43
Develop
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0.0.3
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test_data/createTestData.sh
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test_data/createTestData.sh
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test_data/createTestData.sh
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b2b91ce9
...
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@@ -9,12 +9,12 @@ mkdir -p NEW_test_data
ln
-sfn
`
readlink
-e
./test_data/auth/credential.json
`
~/.deriva/credential.json
mkdir
-p
./NEW_test_data/bag
it
mkdir
-p
./NEW_test_data/bag
singularity run
'docker://bicf/gudmaprbkfilexfer:1.3'
deriva-download-cli dev.gudmap.org
--catalog
2 ./workflow/conf/replicate_export_config.json
.
rid
=
Q-Y5F6
cp
Replicate_Q-Y5F6.zip ./NEW_test_data/bag
it
/Replicate_Q-Y5F6.zip
cp
Replicate_Q-Y5F6.zip ./NEW_test_data/bag/Replicate_Q-Y5F6.zip
mkdir
-p
./NEW_test_data/fastq
unzip ./test_data/bag
it
/Replicate_Q-Y5F6.zip
unzip ./test_data/bag/Replicate_Q-Y5F6.zip
singularity run
'docker://bicf/gudmaprbkfilexfer:1.3'
bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6
cp
Replicate_Q-Y5F6.R1.fastq.gz ./NEW_test_data/fastq/Replicate_Q-Y5F6.R1.fastq.gz
cp
Replicate_Q-Y5F6.R2.fastq.gz ./NEW_test_data/fastq/Replicate_Q-Y5F6.R2.fastq.gz
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