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GUDMAP_RBK
RNA-seq
Commits
c4be8ffc
Commit
c4be8ffc
authored
4 years ago
by
Gervaise Henry
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Change error conditional in bdbag fetch to use file
parent
0f810d4d
Branches
Branches containing commit
Tags
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2 merge requests
!58
Develop
,
!56
Resolve "Detect error in inferMetadata for tracking"
Pipeline
#8873
failed with stages
in 2 minutes and 10 seconds
Changes
1
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1
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1 changed file
workflow/scripts/bdbag_fetch.sh
+6
-5
6 additions, 5 deletions
workflow/scripts/bdbag_fetch.sh
with
6 additions
and
5 deletions
workflow/scripts/bdbag_fetch.sh
+
6
−
5
View file @
c4be8ffc
#!/bin/bash
bdbag
--materialize
${
1
}
--debug
validateError
=
"true"
bdbag
--validate
full
${
1
}
&&
validateError
=
"false"
if
[
"
${
validateError
}
"
==
"true"
]
validate
=
""
bdbag
--validate
full
${
1
}
2> validate.txt
validate
=
$(
tail
-n
validate.txt |
grep
-o
'is valid'
)
if
[
"
${
validate
}
"
!=
"is valid"
]
then
n
=
0
until
[
"
${
n
}
"
-ge
"3"
]
do
bdbag
--resolve-fetch
missing
--validate
full
${
1
}
--debug
&&
validate
Error
=
"false"
&&
break
bdbag
--resolve-fetch
missing
--validate
full
${
1
}
--debug
&&
validate
=
$(
tail
-n
validate.txt |
grep
-o
'is valid'
)
&&
break
n
=
$((
n+1
))
sleep
15
done
fi
if
[
"
${
validate
Error
}
"
=
=
"
true
"
]
if
[
"
${
validate
}
"
!
=
"
is valid
"
]
then
exit
1
fi
...
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