conda YAML files for casc and minced (issue #41 and #42)

workflow/envs/casc.yaml

+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_llvm
+  - blast=2.9.0=h20b68b9_1
+  - boost=1.68.0=py37h8619c78_1001
+  - boost-cpp=1.68.0=h11c811c_1000
+  - bzip2=1.0.8=h516909a_2
+  - ca-certificates=2020.6.20=hecda079_0
+  - certifi=2020.6.20=py37hc8dfbb8_0
+  - gmp=6.2.0=he1b5a44_2
+  - gnutls=3.6.13=h79a8f9a_0
+  - icu=58.2=hf484d3e_1000
+  - ld_impl_linux-64=2.34=h53a641e_5
+  - libblas=3.8.0=16_openblas
+  - libcblas=3.8.0=16_openblas
+  - libffi=3.2.1=he1b5a44_1007
+  - libgcc-ng=9.2.0=h24d8f2e_2
+  - libgfortran-ng=7.5.0=hdf63c60_6
+  - liblapack=3.8.0=16_openblas
+  - libopenblas=0.3.9=h5ec1e0e_0
+  - libstdcxx-ng=9.2.0=hdf63c60_2
+  - llvm-openmp=10.0.0=hc9558a2_0
+  - ncurses=6.1=hf484d3e_1002
+  - nettle=3.4.1=h1bed415_1002
+  - numpy=1.18.5=py37h8960a57_0
+  - openssl=1.1.1g=h516909a_0
+  - pcre=8.44=he1b5a44_0
+  - perl=5.26.2=h516909a_1006
+  - perl-archive-tar=2.32=pl526_0
+  - perl-carp=1.38=pl526_3
+  - perl-common-sense=3.74=pl526_2
+  - perl-compress-raw-bzip2=2.087=pl526he1b5a44_0
+  - perl-compress-raw-zlib=2.087=pl526hc9558a2_0
+  - perl-exporter=5.72=pl526_1
+  - perl-exporter-tiny=1.002001=pl526_0
+  - perl-extutils-makemaker=7.36=pl526_1
+  - perl-io-compress=2.087=pl526he1b5a44_0
+  - perl-io-zlib=1.10=pl526_2
+  - perl-json=4.02=pl526_0
+  - perl-json-xs=2.34=pl526h6bb024c_3
+  - perl-list-moreutils=0.428=pl526_1
+  - perl-list-moreutils-xs=0.428=pl526_0
+  - perl-pathtools=3.75=pl526h14c3975_1
+  - perl-scalar-list-utils=1.52=pl526h516909a_0
+  - perl-types-serialiser=1.0=pl526_2
+  - perl-xsloader=0.24=pl526_0
+  - pip=20.1.1=py_1
+  - python=3.7.6=cpython_h8356626_6
+  - python_abi=3.7=1_cp37m
+  - readline=8.0=hf8c457e_0
+  - setuptools=47.3.1=py37hc8dfbb8_0
+  - sqlite=3.30.1=hcee41ef_0
+  - tk=8.6.10=hed695b0_0
+  - wheel=0.34.2=py_1
+  - xz=5.2.5=h516909a_0
+  - zlib=1.2.11=h516909a_1006

workflow/envs/minced.yaml

+channels:
+  - bioconda
+  - defaults
+dependencies:
+  - java-jdk=7.0.91=1

workflow/rules/annotation.smk

@@ -179,7 +179,7 @@ rule annotation_casc:
     threads:
         config["casc"]["threads"]
     conda:
-        os.path.join(ENV_DIR, "analysis.yaml")
+        os.path.join(ENV_DIR, "casc.yaml")
     shell:
         "(date && "
         "export PATH={config[casc][path]} && "
@@ -199,7 +199,8 @@ rule annotation_minced:
     wildcard_constraints:
         rtype="|".join(READ_TYPES),
         tool="|".join(ASSEMBLERS)
-    conda: "../envs/analysis.yaml"
+    conda:
+        os.path.join(ENV_DIR, "minced.yaml")
     shell:
         "(date && "
         "export PATH={config[minced][path]} && "