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Klinische Genetica
capture-lumc
hutspot
Commits
2ac55fcd
Commit
2ac55fcd
authored
Feb 19, 2019
by
Sander Bollen
Browse files
use pip instead of conda for sanity checks
parent
8ca740f7
Pipeline
#2380
passed with stage
in 36 seconds
Changes
3
Pipelines
1
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Inline
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.gitlab-ci.yml
View file @
2ac55fcd
image
:
python:3.6-stretch
before_script
:
-
export MINICONDA=${HOME}/miniconda
-
export PATH=${MINICONDA}/bin:${PATH}
-
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-
bash miniconda.sh -b -f -p ${MINICONDA}
-
conda config --set always_yes yes
-
conda env create -n my_env -f environment.yml
-
source activate my_env
-
pip install -r requirements.txt
-
pip install -r requirements-dev.txt
test_sanities
:
...
...
requirements.txt
0 → 100644
View file @
2ac55fcd
snakemake
==4.3.0
pyfaidx
==0.5.0
\ No newline at end of file
tests/test_sanity_checks.yml
View file @
2ac55fcd
...
...
@@ -11,79 +11,112 @@
contains
:
-
"
You
must
set
--config
REFERENCE=<path>"
-
name
:
test-reference-does-not-exist
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/teststtest/ REFERENCE=/very/unlikely/to/exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/teststtest/
REFERENCE=/very/unlikely/to/exist
exit_code
:
1
stdout
:
contains
:
-
"
Reference
file
/very/unlikely/to/exist
does
not
exist"
-
name
:
test-no-java
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile
exit_code
:
1
stdout
:
contains
:
-
"
You
must
set
--config
JAVA=<path>"
-
name
:
test-java-does-not-exist
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=/very/unlikely/to/exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=/very/unlikely/to/exist
exit_code
:
1
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
-
name
:
test-no-gatk
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile
exit_code
:
1
stdout
:
contains
:
-
"
You
must
set
--config
GATK=<path>"
-
name
:
test-gatk-does-not-exist
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=/very/unlikely/to/exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=/very/unlikely/to/exist
exit_code
:
1
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
-
name
:
test-no-dbsnp
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile
exit_code
:
1
stdout
:
contains
:
-
"
You
must
set
--config
DBSNP=<path>"
-
name
:
test-dbsnp-does-not-exist
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=/very/unlikely/to/exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile
DBSNP=/very/unlikely/to/exist
exit_code
:
1
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
-
name
:
test-no-onethousand
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
exit_code
:
1
stdout
:
contains
:
-
"
You
must
set
--config
ONETHOUSAND=<path>"
-
name
:
test-onethousand-does-not-exist
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile ONETHOUSAND=/very/unlikely/to/exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
ONETHOUSAND=/very/unlikely/to/exist
exit_code
:
1
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
-
name
:
test-no-hapmap
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile ONETHOUSAND=Snakefile
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
ONETHOUSAND=Snakefile
exit_code
:
1
stdout
:
contains
:
-
"
You
must
set
--config
HAPMAP=<path>"
-
name
:
test-hapmap-does-not-exist
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile ONETHOUSAND=Snakefile HAPMAP=/very/unlikely/to/exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
ONETHOUSAND=Snakefile HAPMAP=/very/unlikely/to/exist
exit_code
:
1
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
-
name
:
test-no-sample-config
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile ONETHOUSAND=Snakefile HAPMAP=Snakefile
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
ONETHOUSAND=Snakefile HAPMAP=Snakefile
exit_code
:
1
stdout
:
contains
:
-
"
You
must
set
--config
SAMPLE_CONFIG=<path>"
-
name
:
test-sample-config-does-not-exist
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/ REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile ONETHOUSAND=Snakefile HAPMAP=Snakefile SAMPLE_CONFIG=/very/unlikely/to/exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
ONETHOUSAND=Snakefile HAPMAP=Snakefile
SAMPLE_CONFIG=/very/unlikely/to/exist
exit_code
:
1
stdout
:
contains
:
...
...
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