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- FROM statonlab/tripal3
- MAINTAINER Zhang Xudong <zhangxudong@genek.cn>
- USER root
- WORKDIR /var/www/html
- RUN set -x \
- # Enable tripal_analysis_blast
- && drush dl -y tripal_analysis_blast \
- # Enable cdetitor and views
- && drush dl -y ckeditor \
- ## && drush en -y ckeditor views_ui \
- # Tripal Daemon
- && cd /var/www/html/sites/all/libraries \
- ## && wget https://github.com/shaneharter/PHP-Daemon/archive/v2.0.tar.gz \
- && wget ftp://gsx.genek.tv/Share/linux_software/PHP-Daemon-2.0.tar.gz \
- ## && tar -zxvf v2.0.tar.gz \
- && tar -zxvf PHP-Daemon-2.0.tar.gz \
- && mv PHP-Daemon-2.0 PHP-Daemon \
- ## && rm v2.0.tar.gz \
- && rm PHP-Daemon-2.0.tar.gz \
- && cd /var/www/html \
- && drush dl drushd \
- ## && drush en -y drushd tripal_daemon \
- # Blast
- && cd /opt \
- && wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.11.0+-x64-linux.tar.gz \
- && tar -zxvf ncbi-blast-2.11.0+-x64-linux.tar.gz \
- && rm ncbi-blast-2.11.0+-x64-linux.tar.gz \
- && cd /var/www/html \
- && git clone http://git.genek.cn:3333/zhxd2/tripal_blast.git sites/all/modules/tripal_blast \
- ## &&drush en -y blast_ui \
- # JBrowse
- && yum-config-manager --disable pgdg94 \
- ## && yum update -y \
- ## && yum upgrade -y perl \
- && yum groupinstall -y "Development Tools" \
- && yum install -y zlib-devel perl-ExtUtils-MakeMaker \
- && mkdir tools \
- && cd tools \
- ## && wget https://github.com/GMOD/jbrowse/releases/download/1.16.11-release/JBrowse-1.16.11.zip \
- && wget ftp://gsx.genek.tv/Share/linux_software/JBrowse-1.16.11.zip \
- && unzip JBrowse-1.16.11.zip \
- && mv JBrowse-1.16.11 JBrowse \
- && cd JBrowse \
- && ./setup.sh \
- && rm ../JBrowse-1.16.11.zip \
- && cd /var/www/html \
- && git clone http://git.genek.cn:3333/zhxd2/tripal_jbrowse.git sites/all/modules/tripal_jbrowse \
- ## && drush en -y tripal_jbrowse_mgmt tripal_jbrowse_page \
- && mkdir -p mydata/raw mydata/blast mydata/jbrowse
- RUN cd /var/www/html/sites/all/modules \
- && git clone https://gitlab.com/mainlabwsu/chado_search.git \
- && cd chado_search/file \
- && cp default.settings.txt settings.conf
- ## && drush pm-enable chado_search
- ##EXPOSE 80 5432
- ##ENTRYPOINT ["init.sh"]
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