From 2762505a5d091952df2294b6d78cc93c1c22a5ee Mon Sep 17 00:00:00 2001 From: Lokesh Sharma Date: Wed, 16 Jan 2019 18:10:44 +0530 Subject: [PATCH 1/7] test --- Dockerfile | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/Dockerfile b/Dockerfile index d04564a..58b5d83 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,16 +1,18 @@ -FROM andrewosh/binder-base - -MAINTAINER Kozo Nishida +FROM jupyter/base-notebook:latest USER root -# Add ecell4 dependencies -RUN apt-get update -RUN apt-get install -y build-essential ruby ruby-dev libzmq3 libzmq3-dev gnuplot-nox libgsl0-dev libtool autoconf automake zlib1g-dev libsqlite3-dev libmagick++-dev imagemagick libatlas-base-dev && apt-get clean -RUN ln -s /usr/bin/libtoolize /usr/bin/libtool # See https://github.com/zeromq/libzmq/issues/1385 +RUN apt-get update && \ + apt-get install -y build-essential \ + ruby2.5 ruby2.5-dev libzmq3-dev gnuplot-nox libgsl-dev libtool autoconf make \ + automake zlib1g-dev libsqlite3-dev libmagick++-dev imagemagick \ + libatlas-base-dev g++ && \ + apt-get clean + -RUN gem update --no-document --system && gem install --no-document sciruby-full +RUN gem install daru nmatrix statsample iruby +# RUN gem update --no-document --system && gem install --no-document sciruby-full -USER main +USER $NB_UID RUN iruby register \ No newline at end of file From e1c25473bc998341dd1e9dce821024e41c4b4e08 Mon Sep 17 00:00:00 2001 From: Lokesh Sharma Date: Wed, 16 Jan 2019 18:57:27 +0530 Subject: [PATCH 2/7] test --- Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 58b5d83..e1ad7c3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,4 +15,6 @@ RUN gem install daru nmatrix statsample iruby USER $NB_UID -RUN iruby register \ No newline at end of file +RUN iruby register + +COPY . . \ No newline at end of file From e83409cd8d1b6fa8feb1f973a22ac4217001ecd9 Mon Sep 17 00:00:00 2001 From: Lokesh Sharma Date: Wed, 16 Jan 2019 19:17:34 +0530 Subject: [PATCH 3/7] test --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index e1ad7c3..fa2a810 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,11 +10,11 @@ RUN apt-get update && \ apt-get clean -RUN gem install daru nmatrix statsample iruby +RUN gem install daru nmatrix statsample cztop iruby # RUN gem update --no-document --system && gem install --no-document sciruby-full USER $NB_UID -RUN iruby register +RUN iruby register --force COPY . . \ No newline at end of file From d329d1d99dfe89de426338709172d1e9e6bcf1b3 Mon Sep 17 00:00:00 2001 From: Lokesh Sharma Date: Thu, 17 Jan 2019 12:07:26 +0530 Subject: [PATCH 4/7] working --- Dockerfile | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index fa2a810..2aed04d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,10 +6,10 @@ RUN apt-get update && \ apt-get install -y build-essential \ ruby2.5 ruby2.5-dev libzmq3-dev gnuplot-nox libgsl-dev libtool autoconf make \ automake zlib1g-dev libsqlite3-dev libmagick++-dev imagemagick \ - libatlas-base-dev g++ && \ + libatlas-base-dev g++ libczmq-dev libffi-dev libtool-bin && \ apt-get clean - +RUN CPPFLAGS='-Wno-error=deprecated-declarations' gem install rbczmq -v '1.7.9' RUN gem install daru nmatrix statsample cztop iruby # RUN gem update --no-document --system && gem install --no-document sciruby-full @@ -17,4 +17,6 @@ USER $NB_UID RUN iruby register --force -COPY . . \ No newline at end of file +COPY . . + +# ENTRYPOINT jupyter-notebook \ No newline at end of file From f7ef564598c738393dc3a54363052565a61bc3b3 Mon Sep 17 00:00:00 2001 From: Lokesh Sharma Date: Thu, 17 Jan 2019 17:28:59 +0530 Subject: [PATCH 5/7] add symengine --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 2aed04d..ad60a98 100644 --- a/Dockerfile +++ b/Dockerfile @@ -9,8 +9,9 @@ RUN apt-get update && \ libatlas-base-dev g++ libczmq-dev libffi-dev libtool-bin && \ apt-get clean +# See https://github.com/methodmissing/rbczmq/issues/64 RUN CPPFLAGS='-Wno-error=deprecated-declarations' gem install rbczmq -v '1.7.9' -RUN gem install daru nmatrix statsample cztop iruby +RUN gem install daru nmatrix cztop iruby symengine # RUN gem update --no-document --system && gem install --no-document sciruby-full USER $NB_UID From 9dcfa57a24e54d7882e77a5ff1abe157724fe450 Mon Sep 17 00:00:00 2001 From: Lokesh Sharma Date: Mon, 21 Jan 2019 11:12:05 +0530 Subject: [PATCH 6/7] install lateast daru --- Dockerfile | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index ad60a98..64f0b1c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,12 +6,15 @@ RUN apt-get update && \ apt-get install -y build-essential \ ruby2.5 ruby2.5-dev libzmq3-dev gnuplot-nox libgsl-dev libtool autoconf make \ automake zlib1g-dev libsqlite3-dev libmagick++-dev imagemagick \ - libatlas-base-dev g++ libczmq-dev libffi-dev libtool-bin && \ + libatlas-base-dev g++ libczmq-dev libffi-dev libtool-bin cmake git && \ apt-get clean # See https://github.com/methodmissing/rbczmq/issues/64 RUN CPPFLAGS='-Wno-error=deprecated-declarations' gem install rbczmq -v '1.7.9' -RUN gem install daru nmatrix cztop iruby symengine +RUN gem install nmatrix daru cztop iruby gnuplotrb gruff +RUN gem install specific_install +RUN gem specific_install https://github.com/SciRuby/daru.git + # RUN gem update --no-document --system && gem install --no-document sciruby-full USER $NB_UID From 1e7662ee632464029ad3c3c41b275832814ff2a5 Mon Sep 17 00:00:00 2001 From: Lokesh Sharma Date: Thu, 24 Jan 2019 18:53:11 +0530 Subject: [PATCH 7/7] install statsample --- Dockerfile | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 64f0b1c..709b823 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,14 +7,18 @@ RUN apt-get update && \ ruby2.5 ruby2.5-dev libzmq3-dev gnuplot-nox libgsl-dev libtool autoconf make \ automake zlib1g-dev libsqlite3-dev libmagick++-dev imagemagick \ libatlas-base-dev g++ libczmq-dev libffi-dev libtool-bin cmake git && \ - apt-get clean + apt-get gnuplot-x11 clean # See https://github.com/methodmissing/rbczmq/issues/64 RUN CPPFLAGS='-Wno-error=deprecated-declarations' gem install rbczmq -v '1.7.9' RUN gem install nmatrix daru cztop iruby gnuplotrb gruff RUN gem install specific_install RUN gem specific_install https://github.com/SciRuby/daru.git +RUN gem install nyaplot +# RUN ls && ls && gem specific_install https://github.com/lokeshh/sciruby.git master +RUN gem install narray nmatrix gsl +RUN gem specific_install https://github.com/lokeshh/statsample-glm.git upgrade_daru # RUN gem update --no-document --system && gem install --no-document sciruby-full USER $NB_UID @@ -23,4 +27,4 @@ RUN iruby register --force COPY . . -# ENTRYPOINT jupyter-notebook \ No newline at end of file +ENTRYPOINT jupyter-notebook \ No newline at end of file