Merge pull request #1070 from griffithlab/dependencies

Remove BigMHC and DeepImmuno as direct dependencies

.github/workflows/tests.yml

@@ -42,6 +42,8 @@ jobs:
         run: |
           pip install polars==0.16.18
           pip install pypandoc==1.7.2
+          pip install git+https://github.com/griffithlab/bigmhc.git#egg=bigmhc
+          pip install git+https://github.com/griffithlab/deepimmuno.git#egg=deepimmuno
           pip install -e .
           mhcflurry-downloads fetch
       - name: List installed packages

docs/install.rst

@@ -118,8 +118,7 @@ install it manually by running:
 
 .. note::
 
-   The ``mhcflurry`` package needs to be installed in the same python 3 conda
-   environment as the ``pvactools`` package.
+   The ``mhcflurry`` package needs to be installed in the same Python 3 environment as the ``pvactools`` package.
 
 Next, you will need to download the download the MHCflurry datasets and trained models:
 
@@ -165,7 +164,7 @@ install it manually by running:
 
 .. note::
 
-   The ``mhcnuggets`` package needs to be installed in the same python 3 conda
+   The ``mhcnuggets`` package needs to be installed in the same Python 3
    environment as the ``pvactools`` package.
 
 You can check that the ``mhcnuggets`` package was installed successfully by running:
@@ -185,6 +184,54 @@ tensorflow manually to version 1.5.0 should solve this problem:
 
    pip install tensorflow==1.5.0
 
+Installing BigMHC
+-----------------
+
+If you wish to run the BigMHC_EL or BigMHC_IM prediction algorithms, you will need to
+install BigMHC on your system. This package not a direct dependency of
+the the ``pvactools`` packages and needs to be installed manually by running:
+
+.. code-block:: none
+
+   pip install git+https://github.com/griffithlab/bigmhc.git#egg=bigmhc
+
+.. note::
+
+   BigMHC needs to be installed in the same python 3
+   environment as the ``pvactools`` package.
+
+You can check that BigMHC was installed successfully by running:
+
+.. code-block:: none
+
+   pip show bigmhc
+
+This should show information about the BigMHC installation.
+
+Installing DeepImmuno
+---------------------
+
+If you wish to run the DeepImmuno prediction algorithm, you will need to
+install DeepImmuno on your system. This package not a direct dependency of
+the the ``pvactools`` packages and needs to be installed manually by running:
+
+.. code-block:: none
+
+   pip install git+https://github.com/griffithlab/deepimmuno.git#egg=deepimmuno
+
+.. note::
+
+   DeepImmuno needs to be installed in the same python 3
+   environment as the ``pvactools`` package.
+
+You can check that DeepImmuno was installed successfully by running:
+
+.. code-block:: none
+
+   pip show deepimmuno
+
+This should show information about the DeepImmuno installation.
+
 .. _blast:
 
 Installing BLAST

setup.py

@@ -90,8 +90,6 @@
         'mhcflurry==2.0.6',
         'testfixtures',
         'polars==0.16.18',
-        'bigmhc @ git+https://github.com/griffithlab/bigmhc.git#egg=bigmhc',
-        'deepimmuno @ git+https://github.com/griffithlab/deepimmuno.git#egg=deepimmuno',
     ],
     package_data={
         'pvactools.tools.pvacseq': pvacseq_data_files,