Snakemake bump 3 11 2

environment.yaml

@@ -0,0 +1,11 @@
+# only put tools that are needed for tests (e.g., `bowtie-build` is needed to make sure
+# that bowtie-index worked), not for the wrappers themselves, which should have
+# their own environment.yml files.
+dependencies:
+  - bioconda::bowtie2 ==2.3.0
+  - bioconda::gffutils ==0.8.7.1
+  - bioconda::hisat2 ==2.0.5
+  - bioconda::pytest ==3.0.5
+  - bioconda::snakemake ==3.11.2
+  - bioconda::samtools ==1.4
+  - lcdb::lcdblib ==0.1

test/test_bowtie2.py

@@ -1,5 +1,4 @@
 import pytest
-import pysam
 from snakemake.shell import shell
 from lcdblib.snakemake import aligners
 from utils import run, dpath, rm, symlink_in_tempdir

test/test_hisat2.py

@@ -1,5 +1,4 @@
 import pytest
-import pysam
 from snakemake.shell import shell
 from lcdblib.snakemake import aligners
 from utils import run, dpath, rm, symlink_in_tempdir

test/test_kallisto.py

@@ -1,6 +1,5 @@
 import pytest
 import json
-import pysam
 from snakemake.shell import shell
 from lcdblib.snakemake import aligners
 from utils import run, dpath, rm, symlink_in_tempdir

travis-setup.sh

@@ -15,5 +15,4 @@ conda config --add channels bioconda
 conda config --add channels lcdb
 
 conda install -y python=3.5
-conda install -y --file requirements.txt
-pip install -r pip-requirements.txt
+conda env update -n root --file environment.yaml

wrappers/bowtie2/align/environment.yaml

@@ -3,5 +3,5 @@ channels:
   - lcdb
 dependencies:
   - bowtie2 ==2.3.0
-  - samtools ==1.3.1
+  - samtools ==1.4
   - lcdblib ==0.1

wrappers/hisat2/align/environment.yaml

@@ -3,5 +3,5 @@ channels:
   - lcdb
 dependencies:
   - hisat2 ==2.0.5
-  - samtools ==1.3.1
+  - samtools ==1.4
   - lcdblib ==0.1

wrappers/rseqc/bam_stat/environment.yaml

@@ -3,3 +3,4 @@ channels:
   - r
 dependencies:
   - rseqc ==2.6.4
+  - pysam ==0.10.0

wrappers/rseqc/geneBody_coverage/environment.yaml

@@ -5,4 +5,5 @@ channels:
   - conda-forge
 dependencies:
   - rseqc ==2.6.4
+  - pysam ==0.10.0
   - r-essentials ==1.5.1

wrappers/rseqc/infer_experiment/environment.yaml

@@ -3,3 +3,4 @@ channels:
   - r
 dependencies:
   - rseqc ==2.6.4
+  - pysam ==0.10.0

wrappers/rseqc/tin/environment.yaml

@@ -3,3 +3,4 @@ channels:
   - r
 dependencies:
   - rseqc ==2.6.4
+  - pysam ==0.10.0

wrappers/samtools/index/environment.yaml

@@ -1,4 +1,4 @@
 channels:
   - bioconda
 dependencies:
-  - samtools ==1.3.1
+  - samtools ==1.4

wrappers/samtools/sort/environment.yaml

@@ -1,4 +1,4 @@
 channels:
   - bioconda
 dependencies:
-  - samtools ==1.3.1
+  - samtools ==1.4