update mykrobe to v0.6.1 (#13566)

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

As this is my first recipe (technically an update, but I effectively had to write from scratch as the program has changed quite a lot) it would be great to have a review from the core team.

recipes/mykrobe/build.sh

@@ -1,3 +1,35 @@
 #!/bin/bash
+set -x
 
-$PYTHON setup.py install --single-version-externally-managed --record=record.txt
+# specify zlib location https://bioconda.github.io/troubleshooting.html#zlib-errors
+export CFLAGS="-I$PREFIX/include"
+export LDFLAGS="-L$PREFIX/lib"
+export CPATH="$PREFIX/include"
+
+# download phelim's fork of mccortex
+MCCORTEX_DIR=mccortex
+MCCORTEX_GIT="https://github.com/phelimb/mccortex"
+mkdir "$MCCORTEX_DIR"
+git clone --recursive -b geno_kmer_count "$MCCORTEX_GIT" "$MCCORTEX_DIR"
+cd "$MCCORTEX_DIR"
+
+# comment this out as it overrides my LDFLAGS variable
+sed -i.bak 's/LDFLAGS  =/#LDFLAGS  =/' libs/htslib/Makefile
+# gcc is hard-coded into Makefile. Comment out to use the conda gcc
+sed -i.bak 's/^CC/#CC/' libs/htslib/Makefile
+
+# point some -lz calls to zlib location
+for make_file in libs/string_buffer/Makefile $(find libs/seq_file -name Makefile) $(find libs/seq-align -name Makefile) Makefile; do
+    sed -i.bak 's/-lz/-lz $(LDFLAGS)/' $make_file
+done
+
+make MAXK=31
+
+mkdir -p $PREFIX/bin
+install -p bin/mccortex31 $PREFIX/bin/
+
+cd ../
+
+"$PYTHON" -m pip install . --no-deps -vv
+
+rm -rf "$MCCORTEX_DIR"

recipes/mykrobe/meta.yaml

@@ -1,40 +1,45 @@
+{% set version = "0.6.1" %}
+
 package:
-  name: mykrobe
-  version: "0.5.6"
+    name   : mykrobe
+    version: {{ version }}
 
 source:
-  url: https://github.com/iqbal-lab/Mykrobe-predictor/archive/933301d9f1e673a2a282255426a885ef72e67c07.tar.gz
-  sha256: adcf75a8e873192047921947ef6c367fadee9dff09637f0acad7a4c9c4bcf53e
+    url    : https://github.com/Mykrobe-tools/mykrobe/archive/{{ version }}.tar.gz
+    sha256 : 5452abf82cb5d3930afc2bc20eaa07b0463403218a1534f036b256dc22aea802
+    md5    : 2650bfab3caa6ac9e142fb19d55f5604
 
 build:
-  # dependency mykatlas currently not built for osx
-  skip: True  # [osx]
-  number: 1
-  entry_points:
-    - mykrobe = mykrobe.mykrobe_predictor:main
+    number: 0
+    skip: True  # [py27]
+    entry_points:
+        - mykrobe = mykrobe.cli:main
 
 requirements:
-  host:
-    - python
-    - setuptools
-
+    build:
+        - {{ compiler('cxx') }}
+    host:
+        - python
+        - pip
+        - zlib
+        - wget
+    run:
+        - python
+        - mongodb >3.0
+        - wget
+        - zlib
 
-  run:
-    - python
-    - mykatlas
-    - ga4ghmongo
-    - mongoengine
-    - future
 test:
-  # Python imports
-  imports:
-    - mykrobe
-  commands:
-    - mykrobe --help
-
+    commands:
+        - mykrobe --version
+        - mykrobe --help
+        - mykrobe predict --help
+        - mykrobe variants --help
+        - mykrobe genotype --help
+        - 'mccortex31 2>&1 | head -n2 | grep "^usage: "'
 
 about:
-  home: https://github.com/iqbal-lab/Mykrobe-predictor
-  license: Custom non-commercial license
-  license_file: LICENSE
-  summary: 'Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.'
+    home: https://github.com/Mykrobe-tools/mykrobe
+    license: MIT
+    license_file: LICENSE
+    summary: 'Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.'

recipes/mykrobe/post-link.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+# This script downloads the panel data that mykrobe uses for its predictions
+
+cd "$PREFIX" || exit 1
+TARBALL="mykrobe-data.tar.gz"
+URLS=(
+    "https://bit.ly/2H9HKTU"
+)
+SHA256="14b4e111d8b17a43dd30e3a55416bab79794ed56c44acc6238e1fd10addd0a03"
+SUCCESS=0
+
+for URL in "${URLS[@]}"; do
+    wget -O - "${URL}" > "$TARBALL"
+    [[ $? == 0 ]] || continue
+
+    if [[ $(shasum -a 256 $TARBALL | cut -f1 -d " ") == "$SHA256" ]]; then
+        SUCCESS=1
+        break
+    fi
+
+done
+
+if [[ $SUCCESS != 1 ]]; then
+    echo "ERROR: post-link.sh was unable to download any of the following URLs with the shasum $SHA256:" >> "${PREFIX}/.messages.txt" 2>&1
+    printf '%s\n' "${URLS[@]}" >> "${PREFIX}/.messages.txt" 2>&1
+    exit 1
+fi
+
+tar -vxzf "$TARBALL"
+rm -fr "$PREFIX"/src/mykrobe/data
+mv mykrobe-data "$PREFIX"/src/mykrobe/data
+rm "$TARBALL"