From 8488af8987c65bbdd3a84fe58c44063fc02922bb Mon Sep 17 00:00:00 2001
From: Marty Kandes <mkandes@sdsc.edu>
Date: Wed, 18 Apr 2018 13:19:22 -0700
Subject: [PATCH] naked-singularity-v0.3.0 :: added biopython for python and
python3 to keras-tensorflow-cpu.def and keras-tensorflow-gpu.def on comet
---
README | 4 ++--
.../sdsc/comet/keras/keras-tensorflow-cpu.def | 15 ++++++++++++---
.../sdsc/comet/keras/keras-tensorflow-gpu.def | 13 +++++++++++--
3 files changed, 25 insertions(+), 7 deletions(-)
diff --git a/README b/README
index 5ae41e9..2cc77b1 100644
--- a/README
+++ b/README
@@ -29,8 +29,8 @@ AUTHOR
VERSION
- 0.2.9
+ 0.3.0
LAST UPDATED
- Wednesday, April 10th, 2018
+ Wednesday, April 18th, 2018
diff --git a/definition-files/us/ucsd/sdsc/comet/keras/keras-tensorflow-cpu.def b/definition-files/us/ucsd/sdsc/comet/keras/keras-tensorflow-cpu.def
index ee9823a..e511bf1 100644
--- a/definition-files/us/ucsd/sdsc/comet/keras/keras-tensorflow-cpu.def
+++ b/definition-files/us/ucsd/sdsc/comet/keras/keras-tensorflow-cpu.def
@@ -12,7 +12,7 @@ OSVersion: xenial
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
- LAST_UPDATED 20180404
+ LAST_UPDATED 20180418
%setup
@@ -203,6 +203,10 @@ OSVersion: xenial
apt-get -y install libopencv-dev
apt-get -y install python-opencv
+ # Install common python packages for the biological and biomedical sciences
+ apt-get -y install python-biopython
+ apt-get -y install python-biopython-sql
+
# Install common python3 packages for data science and machine learning applications
apt-get -y install python3-scipy
apt-get -y install python3-pandas
@@ -214,15 +218,20 @@ OSVersion: xenial
apt-get -y install python3-sklearn
apt-get -y install python3-nltk
+ # Install common python3 packages for the biological and biomedical sciences
+ apt-get -y install python3-biopython
+ apt-get -y install python3-biopython-sql
+
# Install Keras dependencies for python(2) and python3
apt-get -y install python-yaml
apt-get -y install python3-yaml
+
+ cd /opt
# Download, build, and install Keras
- cd /opt
wget https://github.com/keras-team/keras/archive/2.1.5.tar.gz
tar -xzvf 2.1.5.tar.gz
- cd keras-2.1.5
+ cd /opt/keras-2.1.5
python setup.py install
python3 setup.py install
diff --git a/definition-files/us/ucsd/sdsc/comet/keras/keras-tensorflow-gpu.def b/definition-files/us/ucsd/sdsc/comet/keras/keras-tensorflow-gpu.def
index 9480098..ed9e923 100644
--- a/definition-files/us/ucsd/sdsc/comet/keras/keras-tensorflow-gpu.def
+++ b/definition-files/us/ucsd/sdsc/comet/keras/keras-tensorflow-gpu.def
@@ -12,7 +12,7 @@ OSVersion: xenial
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
- LAST_UPDATED 20180405
+ LAST_UPDATED 20180418
%setup
@@ -382,6 +382,10 @@ OSVersion: xenial
apt-get -y install libopencv-dev
apt-get -y install python-opencv
+ # Install common python packages for the biological and biomedical sciences
+ apt-get -y install python-biopython
+ apt-get -y install python-biopython-sql
+
# Install common python3 packages for data science and machine learning applications
apt-get -y install python3-scipy
apt-get -y install python3-pandas
@@ -393,12 +397,17 @@ OSVersion: xenial
apt-get -y install python3-sklearn
apt-get -y install python3-nltk
+ # Install common python3 packages for the biological and biomedical sciences
+ apt-get -y install python3-biopython
+ apt-get -y install python3-biopython-sql
+
# Install Keras dependencies for python(2) and python3
apt-get -y install python-yaml
apt-get -y install python3-yaml
- # Download, build, and install Keras
cd /opt
+
+ # Download, build, and install Keras
wget https://github.com/keras-team/keras/archive/2.1.5.tar.gz
tar -xzvf 2.1.5.tar.gz
cd /opt/keras-2.1.5
--
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