Release 12.4.0 (#398)

* Make consortium releases = public releases, add dashboard plots/tables (#385) * Remove null oncotree codes in consortium release * Filter out flagged mutations * Add to dashboard plot * Correct queries * Subset * Update description * Add figure * Fix * Fix * Add to dashboard * Fix text * Add variant counts * Add index * Add non somatic mutation check * Add headers * Add SNVs that were annotatoed as DNP * Fix * Store as file * Fix * Fix * Fix text * Add spacing * update * Add * Only upload subset * Add in files to release * Don't filter out blacklist variants * Use mutation file * Correct * Edit * Fix * Fix * Update genie/database_to_staging.py * Fix columns * Add * Remove comments * Push * Add 'Not released' value (#389) * Add Not released value * Use stringIO, fix tests * Calculate missing counts (#388) * Calculate missing counts * Fix * Update genie/database_to_staging.py * Add function to calculate missing variant counts * No need for blindtext * Fix * Shuffle sections * Fix * Fix missing variant counts * Fix section * Fix * Fix headers * Fix docker (#396) * Fix docker * Add comment * Fix * Fix * Fix Co-authored-by: EC2 Default User <[email protected]> * update version Co-authored-by: EC2 Default User <[email protected]>
Sage-Bionetworks · Mar 5, 2021 · 757dcc0 · 757dcc0
1 parent 4b496a2
commit 757dcc0
Show file tree

Hide file tree

Showing 6 changed files with 18 additions and 15 deletions.
diff --git a/.dockerignore b/.dockerignore
@@ -1,8 +1,8 @@
 *.txt
+!requirements.txt
 *.bed
 *.csv
 *.tsv
-.dockerignore
 Dockerfile
 db.sqlite3
 __pycache__

diff --git a/Dockerfile b/Dockerfile
@@ -33,23 +33,22 @@ RUN apt-get update && apt-get install -y --allow-unauthenticated \
 # genome nexus
 	openjdk-8-jre
 
-RUN pip3 install --upgrade pip
-RUN pip install synapseclient httplib2 pycrypto PyYAML
-RUN pip install pandas numexpr --upgrade
-
 #install pandoc 1.19.2.1 (dashboard use)
 RUN wget https://github.com/jgm/pandoc/releases/download/1.19.2.1/pandoc-1.19.2.1-1-amd64.deb
 RUN dpkg -i pandoc-1.19.2.1-1-amd64.deb	
 
-COPY R/install_packages.R /install_packages.R
-RUN Rscript /install_packages.R
-
 # Only copy most recent changes in code are always installed
 # Do not build from local computer
 WORKDIR /root/Genie
-COPY ./ ./
-RUN python3 setup.py sdist
-RUN python3 setup.py develop
+COPY . .
+
+ENV CRYPTOGRAPHY_DONT_BUILD_RUST=true
+RUN Rscript R/install_packages.R
+
+RUN pip3 install --no-cache-dir -r requirements.txt
+RUN pip3 install -e .
+# RUN python3 setup.py sdist
+# RUN python3 setup.py develop
 
 WORKDIR /root/
 # Must move this git clone to after the install of Genie,

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +1,2 @@
 include genie/*.sh
+include R/*
diff --git a/R/install_packages.R b/R/install_packages.R
@@ -1,4 +1,4 @@
-install.packages("synapser", repos=c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))
+install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))
 install.packages("dplyr", repos = "http://cran.r-project.org")
 install.packages("argparse", repos = "http://cran.r-project.org")
 install.packages("rmarkdown", repos = "http://cran.r-project.org")
@@ -7,7 +7,6 @@ install.packages("testthat", repos = "http://cran.r-project.org")
 install.packages("xtable", repos = "http://cran.r-project.org")
 install.packages("ggpubr", repos = "http://cran.r-project.org")
 install.packages("XML", repos = "http://cran.r-project.org")
-
 install.packages("BiocManager", repos = "http://cran.r-project.org")
 
 BiocManager::install("VariantAnnotation")

diff --git a/genie/__version__.py b/genie/__version__.py
@@ -1 +1 @@
-__version__ = "12.3.0"
+__version__ = "12.4.0"
diff --git a/requirements.txt b/requirements.txt
@@ -1 +1,5 @@
-synapseclient==2.2.2
+synapseclient>=2.3.0
+pandas>=1.0
+httplib2>=0.11.3
+pycrypto>=2.6.1
+PyYAML>=5.1