search

bgruening / docker-galaxy-stable

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
http://bgruening.github.io/docker-galaxy-stable
MIT License
225 stars 133 forks source link

new tool is missing in the tool bar #177

Closed mictadlo closed 8 years ago

mictadlo commented 8 years ago

Hello, I added the following tools to my Dockerfile:

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name macs21 --panel-section-name NGS:_Peak_Calling_Youtube" \
"--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name rnachipintegrator --panel-section-name NGS:_Peak_Calling_Youtube"

Next, I updated the docker container with the following command:

docker build -t galaxy16.01.1 .

Step 40 : RUN install-repository     "--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name macs21 --panel-section-name NGS:_Peak_Calling_Youtube"     "--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name rnachipintegrator --panel-section-name NGS:_Peak_Calling_Youtube"
---> Running in c5583219e285
* Starting PostgreSQL 9.3 database server
  ...done.
Activating virtualenv at .venv
Ignoring indexes: https://pypi.python.org/simple
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.                                                                                                                    
  SNIMissingWarning                                                                                                                                                                            
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.                                                                                                                                                                                       
  InsecurePlatformWarning                                                                                                                                                                      
Requirement already up-to-date: pip in ./.venv/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9))
Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34))
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35))
Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 37))
Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))
Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))
Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 42))
Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45))
Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))
Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49))
Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))
Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 53))
Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54))
Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58))
Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59))
Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66))
Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.3+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 69))
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.                                                                                                                    
  SNIMissingWarning                                                                                                                                                                            
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.                                                                                                                                                                                       
  InsecurePlatformWarning                                                                                                                                                                      
You are using pip version 8.0.2+gx2, however version 8.1.1 is available.                                                                                                                       
You should consider upgrading via the 'pip install --upgrade pip' command.                                                                                                                     
Requirement already satisfied (use --upgrade to upgrade): psycopg2==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1))
Requirement already satisfied (use --upgrade to upgrade): drmaa in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 2))
You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.                                                                                                                     
Activating virtualenv at .venv
Galaxy is running.
Processing:      --url https://toolshed.g2.bx.psu.edu -o pjbriggs --name macs21 --panel-section-name NGS:_Peak_Calling_Youtube
Response
--------
/api/tool_shed_repositories/21d6abf48ce833a8
  name: macs21
  tool_shed_status: {u'latest_installable_revision': u'True', u'revision_update': u'False', u'revision_upgrade': u'False', u'repository_deprecated': u'False'}
  status: Installed
  deleted: False
  ctx_rev: 0
  error_message: 
  installed_changeset_revision: 06cb587a5e87
  tool_shed: toolshed.g2.bx.psu.edu
  dist_to_shed: False
  id: 21d6abf48ce833a8
  owner: pjbriggs
  uninstalled: False
  changeset_revision: 06cb587a5e87
  includes_datatypes: False
Processing:      --url https://toolshed.g2.bx.psu.edu -o pjbriggs --name rnachipintegrator --panel-section-name NGS:_Peak_Calling_Youtube
Response
--------
/api/tool_shed_repositories/1b134f9a210c0a06
  name: rnachipintegrator
  tool_shed_status: {u'latest_installable_revision': u'True', u'revision_update': u'False', u'revision_upgrade': u'False', u'repository_deprecated': u'False'}
  status: Installed
  deleted: False
  ctx_rev: 1
  error_message: 
  installed_changeset_revision: 5f69a2c1b9c9
  tool_shed: toolshed.g2.bx.psu.edu
  dist_to_shed: False
  id: 1b134f9a210c0a06
  owner: pjbriggs
  uninstalled: False
  changeset_revision: 5f69a2c1b9c9
  includes_datatypes: False
Activating virtualenv at .venv
Ignoring indexes: https://pypi.python.org/simple
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.                                                                                                                    
  SNIMissingWarning                                                                                                                                                                            
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.                                                                                                                                                                                       
  InsecurePlatformWarning                                                                                                                                                                      
Requirement already up-to-date: pip in ./.venv/lib/python2.7/site-packages
Activating virtualenv at .venv
* Stopping PostgreSQL 9.3 database server
  ...done.
---> 2ae2ccce6f61
Removing intermediate container c5583219e285
Step 41 : EXPOSE :80
---> Running in 43b0c9089846
---> 95b407725ac2
Removing intermediate container 43b0c9089846
Step 42 : EXPOSE :21
---> Running in 5e799ad445c6
---> 87cfc1774ffd
Removing intermediate container 5e799ad445c6
Step 43 : EXPOSE :8800
---> Running in fd53db80f4d3
---> f53daea7ee39
Removing intermediate container fd53db80f4d3
Step 44 : EXPOSE :9002
---> Running in aa7d55928557
---> b5ca8e64dded
Removing intermediate container aa7d55928557
Step 45 : ENV HOME $GALAXY_HOME
---> Running in b7fc2b592d04
---> 9f4bd89a4cdb
Removing intermediate container b7fc2b592d04
Step 46 : ENV PYTHONPATH /galaxy-central/lib/
---> Running in 31b44a7fc2c1
---> ea0c6d7fea0a
Removing intermediate container 31b44a7fc2c1
Step 47 : VOLUME /export/ /data/ /var/lib/docker
---> Running in 524abfe787e2
---> 44ba25edbd50
Removing intermediate container 524abfe787e2
Step 48 : CMD /usr/bin/startup
---> Running in bbd2feeed21d
---> b4b050cfa0dd
Removing intermediate container bbd2feeed21d
Successfully built b4b050cfa0dd

docker run -d --net=host --privileged=true -v /home/galaxy/galaxy_storage/:/export -e "GALAXY_LOGGING=full" galaxy16.01.1
4d9c5a733d2c062c20e57607a8ff665edf2d33dd2095d936970b56913c3f507b

Unfortunately, NGS:_Peak_Calling_Youtube does not appear in the tool bar. Furthermore, I could not find the installed tools in Installed tool shed repositories.

What did I do wrong?

Thank you in advance.

mic

bgruening commented 8 years ago

Mic, can you check the admin section if all tools are green? Can you share the Dockerfile if all tools are green? From the logs everything looks fine? Browser cache?

mictadlo commented 8 years ago

@bgruening As soon as I mounted an empty folder -v /home/galaxy/galaxy_storage2/:/export to the container the new tool appeared together with the old ones.

This is my Dockerfile:

# Test

FROM quay.io/bgruening/galaxy:16.01

MAINTAINER auto script

ENV GALAXY_CONFIG_BRAND Kevin's Galaxy
ENV GALAXY_CONFIG_SERVE_XSS_VULNERABLE_MIMETYPES True

WORKDIR /galaxy-central

RUN \
  apt-get update -y && apt-get upgrade -y; \
  apt-get -y install python-software-properties; \
  apt-get -y install software-properties-common; \
  add-apt-repository -y ppa:nebc/bio-linux; \
  apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 36A1D7869245C8950F966E92D8576A8BA88D21E9; \
  apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80 0xcbcb082a1bb943db; \
  add-apt-repository 'deb [arch=amd64,i386] http://mirror.aarnet.edu.au/pub/MariaDB/repo/10.1/ubuntu trusty main'; \
  apt-get update -y;\
  apt-get install --no-install-recommends -y autoconf automake build-essential gfortran cmake git-core libatlas-base-dev libblas-dev liblapack-dev openssl; \
  apt-get install --no-install-recommends -y fort77 xorg-dev liblzma-dev  libblas-dev gfortran gcc-multilib gobjc++ libreadline-dev; \
  apt-get install --no-install-recommends -y libcairo2-dev libxslt-dev; \
  apt-get install --no-install-recommends -y openjdk-7-jre-headless python-dev python-setuptools python-virtualenv zlib1g-dev libyaml-dev subversion pkg-config; \
  apt-get install --no-install-recommends -y wget curl unzip git parallel mercurial python-psycopg2  sudo samtools; \
  apt-get install --no-install-recommends -y nginx-extras=1.4.6-1ubuntu3.3ppa1 nginx-common=1.4.6-1ubuntu3.3ppa1 uwsgi uwsgi-plugin-python supervisor slurm-llnl slurm-llnl-torque libswitch-perl; \
  apt-get install --no-install-recommends -y slurm-drmaa-dev proftpd proftpd-mod-pgsql libyaml-dev nodejs-legacy npm aufs-tools; \
  apt-get install --no-install-recommends -y nano nmap lynx vim curl python-pip python-gnuplot python-rpy2; \
  apt-get install --no-install-recommends -y mariadb-server libmariadbclient-dev postgresql-9.3 pgadmin3 proftpd-mod-pgsql; \
  apt-get clean;

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name hgv_hilbertvis --panel-section-name Phenotype_Association" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name substitution_rates --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_calmd --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_mpileup --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name kernel_canonical_correlation_analysis --panel-section-name Multivariate_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name pileup_parser --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcffilter --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name depth_of_coverage --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name maf_cpg_filter --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name quality_filter --panel-section-name Regional_Variation"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fasta_formatter --panel-section-name FASTA_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_trimmer_by_quality --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name kraken_report --panel-section-name Metagenomic_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name genetrack --panel-section-name NGS:_Peak_Calling" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcffixup --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fasta_filter_by_length --panel-section-name FASTA_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfaddinfo --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfprimers --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name microsats_mutability --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name variants_validate --panel-section-name NGS:_GATK_Tools_(beta)"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name repmatch_gff3 --panel-section-name NGS:_Peak_Calling" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name sicer --panel-section-name NGS:_Peak_Calling" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfflatten --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name lda_analysis --panel-section-name Statistics" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name meme_meme --panel-section-name Motif_Tools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name concat --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o boris --name phylorelatives --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcf2pgsnp --panel-section-name Phenotype_Association" \
"--url https://toolshed.g2.bx.psu.edu -o gregory-minevich --name cloudmap_in_silico_complementation --panel-section-name CloudMap" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name column_maker --panel-section-id textutil"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name print_reads --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_nucleotides_distribution --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfvcfintersect --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fasta_compute_length --panel-section-name FASTA_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name sam_pileup --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name weblogo3 --panel-section-name Motif_Tools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfselectsamples --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name picard --panel-section-name NGS:_Picard" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfcheck --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name mutate_snp_codon --panel-section-name NGS:_Variant_Analysis"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o aaronquinlan --name bedtools --panel-section-name BEDTools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_trimmer --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_rmdup --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_filtration --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name featurecounter --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name merge --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name macs2 --panel-section-name NGS:_Peak_Calling" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name basecoverage --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cummerbund --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name linear_regression --panel-section-name Multiple_regression"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o guru-ananda --name karyotype_plot --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_filter --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_renamer --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name realigner_target_creator --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name count_covariates --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_bedcov --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name bowtie2 --panel-section-name NGS:_Mapping" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_quality_converter --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name tophat2 --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name tabular_to_fastq --panel-section-id convert"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o nick --name allele_counts --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name mine --panel-section-name Statistics" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name sam_merge --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name bam_to_sam --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_groomer --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_quality_boxplot --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name best_regression_subsets --panel-section-name Multiple_regression" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_eval --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o bgruening --name trim_galore --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_reheader --panel-section-name NGS:_SAMtools"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffdiff --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name unified_genotyper --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name join --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcftools_slice --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name short_reads_trim_seq --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name bamtools_filter --panel-section-name NGS:_BamTools" \
"--url https://toolshed.g2.bx.psu.edu -o gregory-minevich --name snp_mapping_using_wgs --panel-section-name CloudMap" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name gffread --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_slice_bam --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_paired_end_joiner --panel-section-name NGS:_QC_and_manipulation"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name short_reads_figure_score --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfgenotypes --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name ucsc_custom_track --panel-section-name Graph/Display_Data" \
"--url https://toolshed.g2.bx.psu.edu -o gregory-minevich --name cloudmap_variant_discovery_mapping --panel-section-name CloudMap" \
"--url https://toolshed.g2.bx.psu.edu -o guru-ananda --name rhmm --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name bamtools_split --panel-section-name NGS:_BamTools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name macs --panel-section-name NGS:_Peak_Calling" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name table_annovar --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o gregory-minevich --name bcftools_view --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfhethom --panel-section-name NGS:_VCF_Manipulation"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcftools_annotate --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name weightedaverage --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name bwa --panel-section-name NGS:_Mapping" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name ctd_batch --panel-section-name Phenotype_Association" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_masker_by_quality --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o bgruening --name sailfish --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name substitutions --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o rnateam --name mafft --panel-section-name Multiple_Alignments" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cluster --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfrandomsample --panel-section-name NGS:_VCF_Manipulation"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_quality_statistics --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name megablast_wrapper --panel-section-name NGS:_Mapping" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name xy_plot --panel-section-name Graph/Display_Data" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_trimmer --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name freebayes --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfallelicprimitives --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name t_test_two_samples --panel-section-name Statistics" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcf2tsv --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_select --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o blankenberg --name naive_variant_caller --panel-section-name NGS:_Variant_Analysis"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name histogram --panel-section-name Graph/Display_Data" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_apply_recalibration --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name get_flanks --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_to_tabular --panel-section-id convert" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fasta_to_tabular --panel-section-name FASTA_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name flanking_features --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name count_gff_features --panel-section-name Statistics" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_artifacts_filter --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name snpfreq --panel-section-name Phenotype_Association" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfannotategenotypes --panel-section-name NGS:_VCF_Manipulation"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fasta_nucleotide_changer --panel-section-name FASTA_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name kraken --panel-section-name Metagenomic_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name rcve --panel-section-name Multiple_regression" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_sort --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_quality_filter --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name annotation_profiler --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name subtract --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_to_fasta --panel-section-id convert" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_stats --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name emboss_5 --panel-section-name EMBOSS"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name meme_fimo --panel-section-name Motif_Tools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_combine --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o peterjc --name venn_list --panel-section-name Graph/Display_Data" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_annotator --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name bwa_wrappers --panel-section-name NGS:_Mapping" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name datamash_transpose --panel-section-name Datamash" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_stats --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name bowtie_wrappers --panel-section-name NGS:_Mapping" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfbedintersect --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name kraken_translate --panel-section-name Metagenomic_Analysis"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name coverage --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_paired_end_splitter --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o gregory-minevich --name ems_variant_density_mapping --panel-section-name CloudMap" \
"--url https://toolshed.g2.bx.psu.edu -o guru-ananda --name heatmap --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name tabular_to_fasta --panel-section-id convert" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name pear --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name datamash_ops --panel-section-name Datamash" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name stringtie --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name microsats_alignment_level --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name trimmomatic --panel-section-name NGS:_QC_and_manipulation"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name kraken_filter --panel-section-name Metagenomic_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name vsearch --panel-section-name Metagenomic_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name hisat2 --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name divide_pg_snp --panel-section-name Phenotype_Association" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfleftalign --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name intersect --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastqtofasta --panel-section-id convert" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfsort --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name subtract_query --panel-section-id group" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name logistic_regression_vif --panel-section-name Multiple_regression"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastqc --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name tabular_to_fasta --panel-section-name FASTA_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name dgidb_annotator --panel-section-name Phenotype_Association" \
"--url https://toolshed.g2.bx.psu.edu -o boris --name filter_on_md --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name windowsplitter --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name getindels_2way --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name sam_bitwise_flag_filter --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o boris --name hetbox --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name kraken2tax --panel-section-name Metagenomic_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name canonical_correlation_analysis --panel-section-name Multivariate_Analysis"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name partialr_square --panel-section-name Multiple_regression" \
"--url https://toolshed.g2.bx.psu.edu -o nick --name sequence_content_trimmer --panel-section-name NGS:_Du_Novo" \
"--url https://toolshed.g2.bx.psu.edu -o miller-lab --name genome_diversity --panel-section-name Genome_Diversity" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name cwpair2 --panel-section-name NGS:_Peak_Calling" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name analyze_covariates --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_flagstat --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name clustalw --panel-section-name Multiple_Alignments" \
"--url https://toolshed.g2.bx.psu.edu -o gregory-minevich --name check_snpeff_candidates --panel-section-name CloudMap" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_barcode_splitter --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name gmaj --panel-section-name Graph/Display_Data"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name principal_component_analysis --panel-section-name Multivariate_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtool_filter2 --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name megablast_xml_parser --panel-section-name NGS:_Mapping" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffnorm --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffmerge --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfdistance --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name correlation --panel-section-name Statistics" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_reverse_complement --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name hgv_fundo --panel-section-name Phenotype_Association" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cd_hit_dup --panel-section-name Metagenomic_Analysis"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o arkarachai-fungtammasan --name str_fm --panel-section-name STR-FM:_Microsatellite_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_collapser --panel-section-name FASTA_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name getindelrates_3way --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name complement --panel-section-name Operate_on_Genomic_Intervals" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name snpeff --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name kernel_principal_component_analysis --panel-section-name Multivariate_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o tyty --name structurefold --panel-section-name NGS:_RNA_Structure" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fasta_to_tabular --panel-section-id convert" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfcombine --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name vegan_fisher_alpha --panel-section-name Metagenomic_Analysis"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfgeno2haplo --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffcompare --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cummerbund_to_tabular --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o boris --name getalleleseq --panel-section-name NGS:_Variant_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffquant --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name ngsutils_bam_filter --panel-section-name NGS:_Peak_Calling" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name plot_from_lda --panel-section-name Statistics" \
"--url https://toolshed.g2.bx.psu.edu -o nick --name duplex --panel-section-name NGS:_Du_Novo" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name freebayes_wrapper --panel-section-name Phenotype_Association" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfbreakcreatemulti --panel-section-name NGS:_VCF_Manipulation"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name lastz --panel-section-name NGS:_Mapping" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name scatterplot --panel-section-name Graph/Display_Data" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name generate_pc_lda_matrix --panel-section-name Statistics" \
"--url https://toolshed.g2.bx.psu.edu -o crs4 --name taxonomy_krona_chart --panel-section-name Metagenomic_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfannotate --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_combiner --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name tophat_fusion_post --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name vegan_rarefaction --panel-section-name Metagenomic_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name cufflinks --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name bamtools --panel-section-name NGS:_BamTools"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name pileup_interval --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name sam2interval --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name indels_3way --panel-section-name Regional_Variation" \
"--url https://toolshed.g2.bx.psu.edu -o bgruening --name diffbind --panel-section-name NGS:_Peak_Calling" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_recalibrator --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fasta_concatenate_by_species --panel-section-name FASTA_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name indel_realigner --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name bedtools --panel-section-name BEDTools" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_clipper --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name varscan_version_2 --panel-section-name NGS:_Variant_Analysis"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfcommonsamples --panel-section-name NGS:_VCF_Manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_collapser --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name bam_to_scidx --panel-section-id convert" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name sam_to_bam --panel-section-name NGS:_SAMtools" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name datamash_reverse --panel-section-name Datamash" \
"--url https://toolshed.g2.bx.psu.edu -o iuc --name vegan_diversity --panel-section-name Metagenomic_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_manipulation --panel-section-name NGS:_QC_and_manipulation" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name filter_transcripts_via_tracking --panel-section-name NGS:_RNA_Analysis" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name table_recalibration --panel-section-name NGS:_GATK_Tools_(beta)" \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_idxstats --panel-section-name NGS:_SAMtools"

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_split --panel-section-name NGS:_SAMtools"

#Assembly
#========

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name abyss --panel-section-name Assembly" \
"--url https://toolshed.g2.bx.psu.edu/ -o anmoljh --name trinityrnaseq --panel-section-name Assembly" \
"--url https://toolshed.g2.bx.psu.edu/ -o anmoljh --name trinitystats --panel-section-name Assembly" \
"--url https://toolshed.g2.bx.psu.edu/ -o anmoljh --name align_and_estimate_abundance --panel-section-name Assembly"

#DeepTools
#=========
RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name deeptools --panel-section-name deepTools"

#ChemicalToolBoX
#===============
#Source: https://raw.githubusercontent.com/bgruening/docker-recipes/master/galaxy-chemicaltoolbox/Dockerfile

#Include all needed scripts and libraries from the host
#compressed archives will be extracted automatically
#ADD ./Jmoleditor.tar.bz2 /galaxy-central/

#Install ChemicalToolBox & one example workflow
RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name unique --panel-section-id filter" \
"--url https://toolshed.g2.bx.psu.edu/ -o bjoern-gruening --name sed_wrapper --panel-section-id textutil" \
"--url https://testtoolshed.g2.bx.psu.edu/ -o bgruening --name chemicaltoolbox --panel-section-name ChemicalToolBox" \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name chemicaltoolbox_merging_chemical_databases_workflow --panel-section-name ChemicalToolBox"

# Differential gene expression analysis
# =====================================
# https://raw.githubusercontent.com/bgruening/docker-recipes/master/galaxy-deseq2/Dockerfile

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name deseq2 --panel-section-name NGS:_RNA-seq" \
"--url https://testtoolshed.g2.bx.psu.edu/ -o iuc --name dexseq --panel-section-name NGS:_RNA-seq" \
"--url https://toolshed.g2.bx.psu.edu/ -o lparsons --name htseq_count --panel-section-name NGS:_RNA-seq"

# Mass spectrometry
# =================

#RUN install-repository \
#    "--url https://testtoolshed.g2.bx.psu.edu/ -o bgruening --name openms --panel-section-name OpenMS"

# SnpSift
# =======
RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name snpsift --panel-section-name SnpSift" \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name snpsift_dbnsfp --panel-section-name SnpSift" \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name snpsift_dbnsfp_datatypes" \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name snpsift_dbnsfp_generic --panel-section-name SnpSift" \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name snpsift_genesets --panel-section-name SnpSift"

#Annotation
#==========
#Source: https://raw.githubusercontent.com/bgruening/docker-galaxy-genome-annotation/master/Dockerfile
#Some basic packages

RUN install-repository \
"--url http://toolshed.g2.bx.psu.edu/ -o iuc --name package_perl_5_18"

#Install NCBI SimilaritySearch

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o devteam --name lastz_paired_reads --panel-section-name NGS:_Mapping" \
"--url https://toolshed.g2.bx.psu.edu/ -o devteam --name ncbi_blast_plus --panel-section-name SimilaritySearch" \
"--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name blast_datatypes" \
"--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name blastxml_to_top_descr --panel-section-name SimilaritySearch" \
"--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name blast_rbh --panel-section-name SimilaritySearch" \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name ncbi_blast_plus --panel-section-name SimilaritySearch" \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name vsearch --panel-section-name SimilaritySearch" \
"--url https://toolshed.g2.bx.psu.edu/ -o devteam --name suite_kraken_0_10_5 --panel-section-name SimilaritySearch" \
"--url https://toolshed.g2.bx.psu.edu/ -o devteam --name cd_hit_dup" \
"--url https://toolshed.g2.bx.psu.edu/ -o cmonjeau --name commet" \
  #  "--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name gi2taxonomy"

#The BLAST2GO database needs to be mounted in manually

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name blast2go --panel-section-name SimilaritySearch" \
"--url https://testtoolshed.g2.bx.psu.edu/ -o bgruening --name diamond --panel-section-name SimilaritySearch" \
"--url https://testtoolshed.g2.bx.psu.edu/ -o bgruening --name data_manager_diamond_database_builder" \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name interproscan5 --panel-section-name SimilaritySearch" \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name augustus --panel-section-name GenePrediction" \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name glimmer3 --panel-section-name GenePrediction" \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name antismash --panel-section-name GeneCluster" \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name minced --panel-section-name CRISPER" \
"--url https://toolshed.g2.bx.psu.edu/ -o jjohnson --name cdhit --panel-section-name SequenceClustering" \
"--url https://toolshed.g2.bx.psu.edu/ -o clustalomega --name clustalomega --panel-section-name SequenceClustering"

RUN apt-get install bedtools

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name macs21 --panel-section-name NGS:_Peak_Calling_Youtube" \
"--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name rnachipintegrator --panel-section-name NGS:_Peak_Calling_Youtube"

# Compile and install kentUtils 
RUN cd /tmp && \
git clone https://github.com/ENCODE-DCC/kentUtils.git && \
cd kentUtils && \
git checkout  v302.1.0 && \
make && \
cp -rp bin/* /usr/local/bin && \
cd .. && rm -rf kentUtils

# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9002 (supvisord web app)
EXPOSE :80
EXPOSE :21
EXPOSE :8800
EXPOSE :9002

# We need to set $HOME for some Tool Shed tools (e.g Perl libs with $HOME/.cpan)
ENV HOME $GALAXY_HOME
ENV PYTHONPATH /galaxy-central/lib/
# Mark folders as imported from the host.
VOLUME ["/export/", "/data/", "/var/lib/docker"]

# Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]

How is it possible to update the Dockerfile without to create an empty mount folder for the container?

Thank you in advance.

Mic

bgruening commented 8 years ago

@mictadlo you are using two different use-cases that are not compatible with each other ... more or less two separate Galaxy instance if I understood you correctly.

Such a Docker file (and this one is a great one ... good work!) creates you a new Galaxy flavour with its own database and tools. If you use a plain Galaxy Docker image and use the export folder you more or less export an entire Galaxy instance to /export, including the database and all tools.

If you know want to use the /export folder (from a different Galaxy Docker flavour) - this is an entire Galaxy installation - with a new Docker flavour it does not work. As you override the internal Galaxy instance by mounting in a new Galaxy instance.

Is this explanation somehow clear?

bgruening commented 8 years ago

@mictadlo I will close this. Please reopen if you still have this issue.

mictadlo commented 8 years ago

Thank you for your explanation.