updates to run on rhino servers

R/utils.r

@@ -10,7 +10,7 @@
 # install any missing packages
 # http://stackoverflow.com/a/19873732/1135316
 if (!suppressMessages(require("pacman"))) install.packages("pacman")
-pacman::p_load(ape, dplyr, ggplot2, stringr, Biostrings, readr, tidyr, seqinr, DECIPHER, functional)
+pacman::p_load(ape, dplyr, ggplot2, stringr, readr, tidyr, seqinr, functional)
 
 # turn off annoying progress bar
 options(dplyr.show_progress=FALSE)

bin/keele

@@ -9,7 +9,7 @@
 if (!suppressMessages(require("pacman"))) install.packages("pacman")
 pacman::p_load(optparse)
 
-search.source <- function(file, path=c('.', '../R', '~/src/matsen/hiv-sim/vidd/R'), ...) 
+search.source <- function(file, path=c('.', 'R'), ...) 
 { 
     for (p in path) { 
         fp <- file.path(p, file) 

docker/Dockerfile

@@ -0,0 +1,96 @@
+# Create an image with that looks like a naive user on the rhino servers.
+#
+# This Dockerfile will compile and install both Beast and
+#
+FROM r-base
+MAINTAINER Chris Warth [email protected]
+
+ENV HOME /root
+WORKDIR ${HOME}
+
+ADD Dockerfile ${HOME}/Dockerfile
+
+RUN apt-get update -qq
+RUN apt-get dist-upgrade -y
+
+# Install tools needed to compile Beast and Beagle.
+# 
+RUN apt-get install -y ant build-essential autoconf automake libtool subversion pkg-config
+
+RUN apt-get install -y \
+    python-dev \
+    wget \
+    openssh-client  \
+    git  \
+    pandoc  \
+    lmodern  \
+    openjdk-7-jdk  \
+    openjdk-7-jre-headless  \
+    cmake  \
+    samtools \
+    freetype* \
+    pkg-config \
+    libcurl4-openssl-dev \
+    libxml2-dev \
+    libssl-dev
+
+RUN wget -q https://bootstrap.pypa.io/get-pip.py
+RUN python get-pip.py
+RUN pip install --upgrade distribute
+
+RUN pip install virtualenv
+
+# # Make ssh dir
+WORKDIR /root
+
+# Make ssh dir
+RUN mkdir /root/.ssh/
+
+# Copy over private key, and set permissions
+ADD id_rsa-github_readonly_user /root/.ssh/id_rsa
+RUN chmod 700  /root/.ssh/id_rsa
+
+# Create known_hosts
+RUN touch /root/.ssh/known_hosts
+
+# Add bitbuckets key
+RUN ssh-keyscan -T 60 github.com >> /root/.ssh/known_hosts
+
+# clone repo and remove private key
+RUN git clone --recursive [email protected]:matsengrp/founder-inference-bakeoff.git
+RUN rm -f /root/.ssh/id_rsa
+
+ADD Dockerfile /root/Dockerfile
+
+# Clone and compile Beagle from sources
+RUN git clone --depth=1 https://github.com/beagle-dev/beagle-lib.git
+WORKDIR ${HOME}/beagle-lib
+RUN ./autogen.sh 
+RUN ./configure --disable-sse --disable-march-native --prefix=/usr/local
+RUN make install
+#RUN rm -rf ${HOME}/beagle-lib
+
+# Clone and install Beast from sources
+WORKDIR ${HOME}
+RUN git clone https://github.com/beast-dev/beast-mcmc.git
+WORKDIR ${HOME}/beast-mcmc
+RUN ant linux
+RUN mv ${HOME}/beast-mcmc/release/Linux/BEASTv1.8.3pre ${HOME}/
+#RUN rm -rf ${HOME}/beast-mcmc
+# this leaves the compiled BEAST jar file in ${HOME}/BEASTv1.8.3pre/
+
+
+# make beagle libraries and Beast script accessible
+RUN echo 'export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH' >> ${HOME}/.bashrc
+ENV LD_LIBRARY_PATH /usr/local/lib:${LD_LIBRARY_PATH}
+
+# make beast scripts accessilbe on PATH
+RUN echo 'export PATH=BEASTv1.8.3pre/bin:$PATH' >> ${HOME}/.bashrc
+
+# Clean-up
+RUN apt-get -y autoremove
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* 
+
+CMD bash
+
+

docker/id_rsa-github_readonly_user

@@ -0,0 +1,27 @@
+-----BEGIN RSA PRIVATE KEY-----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+-----END RSA PRIVATE KEY-----

venv/bin/activate

@@ -39,7 +39,7 @@ deactivate () {
 # unset irrelevant variables
 deactivate nondestructive
 
-VIRTUAL_ENV="/shared/silo_researcher/Matsen_F/MatsenGrp/working/cwarth/founder-inference-bakeoff/venv"
+VIRTUAL_ENV="venv"
 export VIRTUAL_ENV
 
 _OLD_VIRTUAL_PATH="$PATH"

venv/bin/easy_install

@@ -1,4 +1,7 @@
-#!/shared/silo_researcher/Matsen_F/MatsenGrp/working/cwarth/founder-inference-bakeoff/venv/bin/python
+#!/usr/bin/env python2.7
+
+import os; activate_this=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'activate_this.py'); exec(compile(open(activate_this).read(), activate_this, 'exec'), dict(__file__=activate_this)); del os, activate_this
+
 
 # -*- coding: utf-8 -*-
 import re
@@ -8,4 +11,4 @@ from setuptools.command.easy_install import main
 
 if __name__ == '__main__':
     sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())
+    sys.exit(main())

venv/bin/easy_install-2.7

@@ -1,4 +1,7 @@
-#!/shared/silo_researcher/Matsen_F/MatsenGrp/working/cwarth/founder-inference-bakeoff/venv/bin/python
+#!/usr/bin/env python2.7
+
+import os; activate_this=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'activate_this.py'); exec(compile(open(activate_this).read(), activate_this, 'exec'), dict(__file__=activate_this)); del os, activate_this
+
 
 # -*- coding: utf-8 -*-
 import re
@@ -8,4 +11,4 @@ from setuptools.command.easy_install import main
 
 if __name__ == '__main__':
     sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())
+    sys.exit(main())

venv/bin/f2py

@@ -1,4 +1,7 @@
-#!/shared/silo_researcher/Matsen_F/MatsenGrp/working/cwarth/founder-inference-bakeoff/venv/bin/python
+#!/usr/bin/env python2.7
+
+import os; activate_this=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'activate_this.py'); exec(compile(open(activate_this).read(), activate_this, 'exec'), dict(__file__=activate_this)); del os, activate_this
+
 # See http://cens.ioc.ee/projects/f2py2e/
 import os
 import sys
@@ -23,4 +26,4 @@ elif mode == "2e-numpy":
 else:
     sys.stderr.write("Unknown mode: " + repr(mode) + "\\n")
     sys.exit(1)
-main()
+main()

venv/bin/pip

@@ -1,4 +1,7 @@
-#!/shared/silo_researcher/Matsen_F/MatsenGrp/working/cwarth/founder-inference-bakeoff/venv/bin/python
+#!/usr/bin/env python2.7
+
+import os; activate_this=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'activate_this.py'); exec(compile(open(activate_this).read(), activate_this, 'exec'), dict(__file__=activate_this)); del os, activate_this
+
 
 # -*- coding: utf-8 -*-
 import re
@@ -8,4 +11,4 @@ from pip import main
 
 if __name__ == '__main__':
     sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())
+    sys.exit(main())

venv/bin/pip2

@@ -1,4 +1,7 @@
-#!/shared/silo_researcher/Matsen_F/MatsenGrp/working/cwarth/founder-inference-bakeoff/venv/bin/python
+#!/usr/bin/env python2.7
+
+import os; activate_this=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'activate_this.py'); exec(compile(open(activate_this).read(), activate_this, 'exec'), dict(__file__=activate_this)); del os, activate_this
+
 
 # -*- coding: utf-8 -*-
 import re
@@ -8,4 +11,4 @@ from pip import main
 
 if __name__ == '__main__':
     sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())
+    sys.exit(main())

venv/bin/pip2.7

@@ -1,4 +1,7 @@
-#!/shared/silo_researcher/Matsen_F/MatsenGrp/working/cwarth/founder-inference-bakeoff/venv/bin/python
+#!/usr/bin/env python2.7
+
+import os; activate_this=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'activate_this.py'); exec(compile(open(activate_this).read(), activate_this, 'exec'), dict(__file__=activate_this)); del os, activate_this
+
 
 # -*- coding: utf-8 -*-
 import re
@@ -8,4 +11,4 @@ from pip import main
 
 if __name__ == '__main__':
     sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())
+    sys.exit(main())