use pip instead of conda for sanity checks

.gitlab-ci.yml

 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

+snakemake==4.3.0
+pyfaidx==0.5.0
\ No newline at end of file

tests/test_sanity_checks.yml

@@ -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: