Commit 2ac55fcd authored by Sander Bollen's avatar Sander Bollen
Browse files

use pip instead of conda for sanity checks

parent 8ca740f7
Pipeline #2380 passed with stage
in 36 seconds
image: python:3.6-stretch image: python:3.6-stretch
before_script: before_script:
- export MINICONDA=${HOME}/miniconda - pip install -r requirements.txt
- export PATH=${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-dev.txt - pip install -r requirements-dev.txt
test_sanities: test_sanities:
......
snakemake==4.3.0
pyfaidx==0.5.0
\ No newline at end of file
...@@ -11,79 +11,112 @@ ...@@ -11,79 +11,112 @@
contains: contains:
- "You must set --config REFERENCE=<path>" - "You must set --config REFERENCE=<path>"
- name: test-reference-does-not-exist - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "Reference file /very/unlikely/to/exist does not exist" - "Reference file /very/unlikely/to/exist does not exist"
- name: test-no-java - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "You must set --config JAVA=<path>" - "You must set --config JAVA=<path>"
- name: test-java-does-not-exist - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "/very/unlikely/to/exist does not exist" - "/very/unlikely/to/exist does not exist"
- name: test-no-gatk - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "You must set --config GATK=<path>" - "You must set --config GATK=<path>"
- name: test-gatk-does-not-exist - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "/very/unlikely/to/exist does not exist" - "/very/unlikely/to/exist does not exist"
- name: test-no-dbsnp - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "You must set --config DBSNP=<path>" - "You must set --config DBSNP=<path>"
- name: test-dbsnp-does-not-exist - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "/very/unlikely/to/exist does not exist" - "/very/unlikely/to/exist does not exist"
- name: test-no-onethousand - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "You must set --config ONETHOUSAND=<path>" - "You must set --config ONETHOUSAND=<path>"
- name: test-onethousand-does-not-exist - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "/very/unlikely/to/exist does not exist" - "/very/unlikely/to/exist does not exist"
- name: test-no-hapmap - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "You must set --config HAPMAP=<path>" - "You must set --config HAPMAP=<path>"
- name: test-hapmap-does-not-exist - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "/very/unlikely/to/exist does not exist" - "/very/unlikely/to/exist does not exist"
- name: test-no-sample-config - 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 exit_code: 1
stdout: stdout:
contains: contains:
- "You must set --config SAMPLE_CONFIG=<path>" - "You must set --config SAMPLE_CONFIG=<path>"
- name: test-sample-config-does-not-exist - 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 exit_code: 1
stdout: stdout:
contains: contains:
......
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