Merge branch 'develop' into 'master'

Release v0.5.0

See merge request tron/addannot!164

.gitignore

@@ -2,6 +2,7 @@
 .idea
 venv-win
 venv
+venv37
 .env
 dist
 build/*
@@ -11,3 +12,9 @@ neofox/tests/resources/output*
 docs/build
 .ipynb_checkpoints
 neofox-dask-report*
+.tox
+venv*
+py36
+/netMHCIIpan-3.2.Linux.tar.gz
+/netMHCIIpan-4.0.Linux.tar.gz
+/netMHCpan-4.1b.Linux.tar.gz

.gitlab-ci.yml

@@ -16,13 +16,14 @@
 ##
 ## You should have received a copy of the GNU General Public License
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.##
-image: python:3.7-buster
+
+# this image contains multiple Python interpreters
+image: fkrull/multi-python:bionic
 
 # Change pip's cache directory to be inside the project directory since we can
 # only cache local items.
 variables:
-    PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
-    VENV_CACHE_DIR: "$CI_PROJECT_DIR/venv"
+    TOX_CACHE_DIR: "$CI_PROJECT_DIR/.tox"
 
 # Pip's cache doesn't store the python packages
 # https://pip.pypa.io/en/stable/reference/pip_install/#caching
@@ -31,24 +32,40 @@ variables:
 # them in a virtualenv and cache it as well.
 cache:
   paths:
-    - $PIP_CACHE_DIR
-    - $VENV_CACHE_DIR
+    - $TOX_CACHE_DIR
 
 before_script:
   - apt-get update
   - apt-get --assume-yes install gcc gfortran build-essential wget libfreetype6-dev libpng-dev libopenblas-dev
   - python -V
-  - pip install virtualenv
-  - virtualenv venv
-  - source venv/bin/activate
 
 stages:
+  - validation
   - test
+  - deploy
+
+check_version_changes:
+  stage: validation
+  script:
+    # if the version number does not change between this branch and develop it fails
+    - git fetch origin develop
+    - if git diff origin/develop -- neofox/__init__.py | grep VERSION; then exit 0; else echo "Version needs to be increased!"; exit -1; fi
+  except:
+    - develop
+    - master
 
 test:
   stage: test
   script:
-    - python setup.py bdist_wheel
-    - pip uninstall -y neofox
-    - pip install dist/neofox-*.whl
-    - python -m unittest discover neofox.tests.unit_tests
+    - pip install virtualenv tox==3.23.0 tox-wheel==0.6.0
+    - tox
+
+publish_package:
+  stage: deploy
+  script:
+    - pip install twine
+    - python3 setup.py sdist bdist_wheel
+    - TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python -m twine upload --repository-url https://gitlab.rlp.net/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+  only:
+    - develop
+    - master

Dockerfile

@@ -15,8 +15,8 @@ COPY requirements.txt requirements.txt
 COPY LICENSE LICENSE
 COPY README.md README.md
 # these two files will need to be downloaded from the owner's site after agreeing their license
-COPY netMHCIIpan-3.2.Linux.tar.gz netMHCIIpan-3.2.Linux.tar.gz
-COPY netMHCpan-4.0a.Linux.tar.gz netMHCpan-4.0a.Linux.tar.gz
+COPY netMHCIIpan-4.0.Linux.tar.gz netMHCIIpan-4.0.Linux.tar.gz
+COPY netMHCpan-4.1b.Linux.tar.gz netMHCpan-4.1b.Linux.tar.gz
 
 # build and install neofox package
 RUN python3 setup.py bdist_wheel
@@ -36,23 +36,23 @@ ENV NEOFOX_MAKEBLASTDB /app/ncbi-blast-2.10.1+/bin/makeblastdb
 RUN echo $NEOFOX_MAKEBLASTDB
 
 # install netmhcpan
-RUN tar -xvf netMHCpan-4.0a.Linux.tar.gz
+RUN tar -xvf netMHCpan-4.1b.Linux.tar.gz
 RUN echo $NEOFOX_MAKEBLASTDB
-RUN sed -i 's/\/usr\/cbs\/packages\/netMHCpan\/4.0\/netMHCpan-4.0/\/app\/netMHCpan-4.0/g' /app/netMHCpan-4.0/netMHCpan
-RUN sed -i 's/\/scratch/\/app\/netMHCpan-4.0\/tmp/g' /app/netMHCpan-4.0/netMHCpan
-RUN mkdir /app/netMHCpan-4.0/tmp
-RUN wget http://www.cbs.dtu.dk/services/NetMHCpan-4.0/data.Linux.tar.gz  -O /app/netMHCpan-4.0/data.Linux.tar.gz
-RUN tar -xvf /app/netMHCpan-4.0/data.Linux.tar.gz -C /app/netMHCpan-4.0
-ENV NEOFOX_NETMHCPAN /app/netMHCpan-4.0/netMHCpan
+RUN sed -i 's/\/net\/sund-nas.win.dtu.dk\/storage\/services\/www\/packages\/netMHCpan\/4.1\/netMHCpan-4.1/\/app\/netMHCpan-4.1/g' /app/netMHCpan-4.1/netMHCpan
+RUN sed -i 's/ \/tmp/ \/app\/netMHCpan-4.1\/tmp/g' /app/netMHCpan-4.1/netMHCpan
+RUN mkdir /app/netMHCpan-4.1/tmp
+RUN wget https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz  -O /app/netMHCpan-4.1/data.Linux.tar.gz
+RUN tar -xvf /app/netMHCpan-4.1/data.Linux.tar.gz -C /app/netMHCpan-4.1
+ENV NEOFOX_NETMHCPAN /app/netMHCpan-4.1/netMHCpan
 
 # install netmhc2pan
-RUN tar -xvf netMHCIIpan-3.2.Linux.tar.gz
-RUN sed -i 's/\/usr\/cbs\/bio\/src\/netMHCIIpan-3.2/\/app\/netMHCIIpan-3.2/g' /app/netMHCIIpan-3.2/netMHCIIpan
-RUN sed -i 's/\/scratch/\/app\/netMHCIIpan-3.2\/tmp/g' /app/netMHCIIpan-3.2/netMHCIIpan
-RUN mkdir /app/netMHCIIpan-3.2/tmp
-RUN wget http://www.cbs.dtu.dk/services/NetMHCIIpan-3.2/data.Linux.tar.gz -O /app/netMHCIIpan-3.2/data.Linux.tar.gz
-RUN tar -xvf /app/netMHCIIpan-3.2/data.Linux.tar.gz -C /app/netMHCIIpan-3.2
-ENV NEOFOX_NETMHC2PAN /app/netMHCIIpan-3.2/netMHCIIpan
+RUN tar -xvf netMHCIIpan-4.0.Linux.tar.gz
+RUN sed -i 's/\/net\/sund-nas.win.dtu.dk\/storage\/services\/www\/packages\/netMHCIIpan\/4.0\/netMHCIIpan-4.0/\/app\/netMHCIIpan-4.0/g' /app/netMHCIIpan-4.0/netMHCIIpan
+RUN sed -i 's/ \/tmp\//\/app\/netMHCIIpan-4.0\/tmp/g' /app/netMHCIIpan-4.0/netMHCIIpan
+RUN mkdir /app/netMHCIIpan-4.0/tmp
+RUN wget http://www.cbs.dtu.dk/services/NetMHCIIpan-4.0/data.tar.gz -O /app/netMHCIIpan-4.0/data.tar.gz
+RUN tar -xvf /app/netMHCIIpan-4.0/data.tar.gz -C /app/netMHCIIpan-4.0
+ENV NEOFOX_NETMHC2PAN /app/netMHCIIpan-4.0/netMHCIIpan
 RUN apt-get install tcsh
 
 # install mixmhcpred
@@ -68,6 +68,12 @@ RUN wget https://github.com/GfellerLab/MixMHC2pred/archive/v1.2.tar.gz
 RUN tar -xvf v1.2.tar.gz
 ENV NEOFOX_MIXMHC2PRED /app/MixMHC2pred-1.2/MixMHC2pred_unix
 
+# install prime
+RUN wget https://github.com/GfellerLab/PRIME/archive/master.tar.gz
+RUN tar -xvf master.tar.gz
+RUN sed -i 's/\/app\/PRIME/\/app\/PRIME-master/g' /app/PRIME-master/PRIME
+ENV NEOFOX_PRIME /app/PRIME-master/PRIME
+
 # configure references
 RUN apt-get install -y --no-install-recommends build-essential
 RUN neofox-configure --reference-folder /app/neofox-reference --install-r-dependencies

README.md

@@ -24,17 +24,19 @@ NeoFox annotates neoantigen candidate sequences with published neo-epitope descr
 | Priority score                                          | Bjerregaard et al, 2017, Cancer Immunol Immunother.                      | https://doi.org/10.1007/s00262-017-2001-3                                                 |
 | Tcell predictor                                         | Besser et al, 2019, Journal for ImmunoTherapy of Cancer                  | https://doi.org/10.1186/s40425-019-0595-z                                                 |
 | neoag                                                   | Smith et al, 2019, Cancer Immunology Research                            | https://doi.org/10.1158/2326-6066.CIR-19-0155                                             |
+| PRIME                                                   | Schmidt et al., 2021, Cell Reports Medicine                            | https://doi.org/10.1016/j.xcrm.2021.100194                                             |
 
 ## NeoFox Requirements
 
 **Required Software/Tools/Dependencies:**  
-- Python 3.7
+- Python >=3.6, <=3.8
 - R 3.6.0
 - BLAST 2.10.1
 - netMHCpan 4.0
 - netMHCIIpan 3.2
 - MixMHCpred 2.1
 - MixMHC2pred 1.2
+- PRIME 1.0
 
 
 ## Usage from the command line

docs/figures/neofox_model.drawio

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