Merge pull request #408 from apriltuesday/conda-doc

Conda documentation

README.md

@@ -52,6 +52,19 @@ nextflow run ${CODE_ROOT}/pipelines/annotation_pipeline.nf \
   --mappings ${LATEST_MAPPINGS}
 ```
 
+### Conda
+
+You can also install CMAT using Conda.
+For example the following installs CMAT in a new environment called `cmat`, activates the environment, and prints usage:
+```bash
+conda create -n cmat -c conda-forge -c bioconda cmat
+conda activate cmat
+cmat
+```
+
+Note that with conda installation you can't invoke the pipelines directly via Nextflow, so you will need to use the corresponding `cmat` commands - e.g. `cmat annotate` instead of `nextflow run annotation_pipeline.nf`.
+All the same command line options apply.
+
 ## Run
 
 CMAT includes a main annotation pipeline (which also performs consequence and gene mapping), as well as two pipelines to help manage trait mapping curation.
@@ -72,6 +85,7 @@ cd ${ANNOTATION_ROOT}
 mkdir -p gene_mapping logs
 
 # Run the nextflow pipeline, resuming execution of previous attempt if possible.
+# For conda, use instead: cmat annotate
 nextflow run ${CODE_ROOT}/pipelines/annotation_pipeline.nf \
   --output_dir ${ANNOTATION_ROOT} \
   --mappings ${LATEST_MAPPINGS} \
@@ -103,6 +117,7 @@ mkdir -p ${CURATION_ROOT}
 cd ${CURATION_ROOT}
 
 # Run the nextflow pipeline, resuming execution of previous attempt if possible.
+# For conda, use instead: cmat generate-curation
 nextflow run ${CODE_ROOT}/pipelines/generate_curation_spreadsheet.nf \
   --curation_root ${CURATION_ROOT} \
   --mappings ${LATEST_MAPPINGS} \
@@ -130,6 +145,7 @@ Download the spreadsheet as a CSV file, making sure that all the data is visible
 cd ${CURATION_ROOT}
 
 # Run the nextflow pipeline, resuming execution of previous attempt if possible.
+# For conda, use instead: cmat export-curation
 nextflow run ${CODE_ROOT}/pipelines/export_curation_spreadsheet.nf \
   --input_csv ${CURATION_ROOT}/finished_curation_spreadsheet.csv \
   --curation_root ${CURATION_ROOT} \

conda/meta.yaml

@@ -1,54 +1,57 @@
+{% set name = "cmat" %}
 {% set version = "3.1.0" %}
 
 package:
-  name: cmat
+  name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz
-  sha256: 29bdeb28674486785c5f5825afa7d1237bd5dd2c76923145d68543f3a6bb5594
+  sha256: 1e46a83d3d7e46a41f9f62ff4af0c151851fbbebc1c6b129255f987d75b64079
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   host:
     - nextflow >=21.10
     - python >=3.8,<3.10  # restriction from biopython
-    # From requirements.txt
-    - biopython==1.77
-    - coverage==6.5.0
-    - coveralls==3.3.1
-    - jsonschema==3.2.0
-    - numpy==1.24.3
-    - pandas==1.5.3
-    - pytest==7.2.2
-    - pytest-cov==2.10.0
-    - requests==2.31.0
-    - requests-mock==1.8.0
-    - retry==0.9.2
+    - biopython ==1.77
+    - coverage ==6.5.0
+    - coveralls ==3.3.1
+    - jsonschema ==3.2.0
+    - numpy ==1.24.3
+    - pandas ==1.5.3
+    - pytest ==7.2.2
+    - pytest-cov ==2.10.0
+    - requests ==2.31.0
+    - requests-mock ==1.8.0
+    - retry ==0.9.2
   run:
     - nextflow >=21.10.0
     - python >=3.8,<3.10
-    - biopython==1.77
-    - coverage==6.5.0
-    - coveralls==3.3.1
-    - jsonschema==3.2.0
-    - numpy==1.24.3
-    - pandas==1.5.3
-    - pytest==7.2.2
-    - pytest-cov==2.10.0
-    - requests==2.31.0
-    - requests-mock==1.8.0
-    - retry==0.9.2
+    - biopython ==1.77
+    - coverage ==6.5.0
+    - coveralls ==3.3.1
+    - jsonschema ==3.2.0
+    - numpy ==1.24.3
+    - pandas ==1.5.3
+    - pytest ==7.2.2
+    - pytest-cov ==2.10.0
+    - requests ==2.31.0
+    - requests-mock ==1.8.0
+    - retry ==0.9.2
 
 test:
   imports:
     - cmat
   commands:
     - cmat
-    - cmat annotate --help
+    # rm to avoid this: https://github.com/bioconda/bioconda-utils/issues/172
+    - cmat annotate --help && rm -rf .nextflow
 
 about:
   home: https://github.com/EBIvariation/CMAT