How would one go about getting the current Main instance running locally?

**Updated to reflect recent changes to galaxy-cloudman-playbook**

Hi Jeremy,

A script to do just that is available with the galaxy-cloudman-playbook

https://github.com/galaxyproject/galaxy-cloudman-playbook/tree/master/roles/galaxyprojectdotorg.cloudman-galaxy-setup/files/scripts

This works with a standard local installation. You can skip all the ansible stuff and just run the install script using the instructions below

Start with a fresh Galaxy installation and database

Modify Galaxy

curl https://raw.githubusercontent.com/galaxyproject/galaxy-cloudman-playbook/master/roles/galaxyprojectdotorg.cloudman-galaxy-setup/files/galaxy/shed_tool_conf.xml.cloud > config/tool_conf.xml 

Uncomment and alter this line in galaxy.ini

tool_config_file = config/tool_conf.xml,config/tool_conf.xml.main

Configure and Run Galaxy Cloudman Playbook

git clone https://github.com/galaxyproject/galaxy-cloudman-playbook.git
cd galaxy-cloudman-playbook/roles/galaxyprojectdotorg.cloudman-galaxy-setup/files/scripts

pip install bioblend

ln -s ../../../../files/shed_tool_list.yaml.cloud .

configure the shed_tool_list.yaml.cloud with your Galaxy url and admin user API (obtained from your Galaxy instance web app)

python install_tool_shed_tools.py -t shed_tool_list.yaml.cloud

A couple caveats:

If this the app server is running Galaxy from a directory make sure the IP in your conf file ends in a slash e.g. 10.30.4.241/galaxy/

You will need to enable API access, so if you are using external authentication like LDAP an explicit Apache or nginx section might be required to allow this.

<Location "/galaxy/api">                                                                                                                                                         
    Satisfy Any                                                                                                                                                       
    Allow from all                                                                                                                                                     
</Location>

Expect a ton of InsecureRequestWarnings. There are "operation not permitted" errors even if you run this as root.

Put your shed_tool_conf.xml and shed_tool_data_table_conf.xml in version control since these will be altered by the script.

Hello,

You can start here: http://getgalaxy.org

The instructions continue from there for how to set up a production instance. Tools are obtained from the Tool Shed. A local will take significant resources to do the same types of analysis that are set up Main, but this is something you may already know.

If the server is for your own use (or a smaller group), then a cloud version could be a better solution: http://usegalaxy.org/cloud

All choices:
http://wiki.galaxyproject.org/BigPicture/Choices

A list of other groups that have set up public Galaxy instances:
http://wiki.galaxyproject.org/PublicGalaxyServers

And there is active deployment and development discussion going on at the galaxy-dev at galaxyproject dot org mailing list:
http://wiki.galaxyproject.org/MailingLists

Best, Jen, Galaxy team

Hi Jen and Enis

I have tried to follow this but have run into a number of issues:

I could not find an example so used shed_tool_list.yaml.cloud

wget https://github.com/mdshw5/cloudman-image-playbook/blob/master/scripts/shed_tool_list.yaml.cloud

running works, up to a point.

rerunning it shows

python install_tool_shed_tools.py -t shed_tool_list.yaml.cloud^M

(1/206) Tool all_cufflinks_tool_suite already installed. Skipping...^M^M

(2/206) Tool all_vcftools already installed. Skipping...^M^M

.

.

164/206) Installing tool suite_gatk_1_4 from devteam to section gatk (TRT: 0:00:04.112586)^M^M

        Tool installing.^M^M

        Tool suite_gatk_1_4 installed successfully (in 0:00:20.647678) at revision 3e6a4fcbf335^M^M

(165/206) Installing tool suite_gops_1_0 from devteam to section bxops (TRT: 0:00:25.878629)^M^M

        * Error installing a tool (after suite_gops_1_0)! Name: 0:00:08.197327,owner: devteam, revision: c82347870270, error: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}^M^M

(166/206) Installing tool suite_samtools_0_1_18 from devteam to section samtools (TRT: 0:00:35.193715)^M^M

        * Error installing a tool (after suite_samtools_0_1_18)! Name: 0:00:05.967991,owner: devteam, revision: 71d378848982, error: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}^M^M

(167/206) Tool suite_samtools_0_1_19 already installed. Skipping...^M

..

.

(202/206) Installing tool weblogo3 from devteam to section plots (TRT: 0:00:47.618287)^M^M

        Tool installing.^M^M

        Tool weblogo3 installed successfully (in 0:00:24.286027) at revision a10f9ed463ae^M^M

(203/206) Tool weightedaverage already installed. Skipping...^M^M

(204/206) Tool windowsplitter already installed. Skipping...^M^M

(205/206) Tool xy_plot already installed. Skipping...^M^M

(206/206) Tool data_manager_fetch_genome_all_fasta already installed. Skipping...^M^M

Skipped tools (201): [u'all_cufflinks_tool_suite', u'all_vcftools', u'analyze_covariates', u'annotation_profiler', u'bamleftalign', u'bam_to_sam', u'basecoverage', u'bcftools', u'best_regression_subsets', u'bowtie2', u'bowtie_color_wrappers', u'bowtie_wrappers', u'bwa_0_7_10', u'bwa_wrappers', u'categorize_elements_satisfying_criteria', u'ccat', u'change_case', u'clustalw', u'cluster', u'column_maker', u'complement', u'compute_motif_frequencies_for_all_motifs', u'compute_motifs_frequency', u'compute_q_values', u'concat', u'condense_characters', u'convert_characters', u'correlation', u'count_covariates', u'count_gff_features', u'coverage', u'ctd_batch', u'cuffcompare', u'cuffdiff', u'cufflinks', u'cuffmerge', u'cut_columns', u'depth_of_coverage', u'dgidb_annotator', u'divide_pg_snp', u'dna_filtering', u'draw_stacked_barplots', u'dwt_cor_ava_perclass', u'dwt_cor_avb_all', u'dwt_ivc_all', u'dwt_var_perclass', u'dwt_var_perfeature', u'emboss_5', u'emboss_datatypes', u'express', u'fasta_clipping_histogram', u'fasta_compute_length', u'fasta_concatenate_by_species', u'fasta_filter_by_length', u'fasta_formatter', u'fasta_nucleotide_changer', u'fasta_to_tabular', u'fastqc', u'fastq_combiner', u'fastq_filter', u'fastq_groomer', u'fastq_manipulation', u'fastq_masker_by_quality', u'fastq_paired_end_deinterlacer', u'fastq_paired_end_interlacer', u'fastq_paired_end_joiner', u'fastq_paired_end_splitter', u'fastq_quality_boxplot', u'fastq_quality_converter', u'fastq_quality_filter', u'fastqsolexa_to_fasta_qual', u'fastq_stats', u'fastqtofasta', u'fastq_to_fasta', u'fastq_to_tabular', u'fastq_trimmer', u'fastq_trimmer_by_quality', u'fastx_artifacts_filter', u'fastx_barcode_splitter', u'fastx_clipper', u'fastx_collapser', u'fastx_nucleotides_distribution', u'fastx_quality_statistics', u'fastx_renamer', u'fastx_reverse_complement', u'fastx_trimmer', u'featurecounter', u'filter_transcripts_via_tracking', u'find_diag_hits', u'flanking_features', u'freebayes', u'freebayes_0_9_14_8a407cf5f4', u'freebayes_wrapper', u'gatk2', u'generate_pc_lda_matrix', u'get_flanks', u'getindelrates_3way', u'getindels_2way', u'gi2taxonomy', u'gmaj', u'hgv_fundo', u'hgv_hilbertvis', u'histogram', u'indel_realigner', u'indels_3way', u'intersect', u'join', u'lastz', u'lastz_paired_reads', u'lca_wrapper', u'lda_analysis', u'linear_regression', u'logistic_regression_vif', u'macs', u'maf_cpg_filter', u'merge', u'merge_cols', u'microsatellite_birthdeath', u'microsats_alignment_level', u'microsats_mutability', u'mine', u'multispecies_orthologous_microsats', u'mutate_snp_codon', u'ncbi_blast_plus', u'partialr_square', u'pearson_correlation', u'pgsnp2gd_snp', u'picard', u'pileup_interval', u'pileup_parser', u'plot_from_lda', u'poisson2test', u'principal_component_analysis', u'print_reads', u'quality_filter', u'rcve', u'realigner_target_creator', u'remove_beginning', u'sam2interval', u'sam_bitwise_flag_filter', u'sam_merge', u'sam_pileup', u'sam_to_bam', u'samtool_filter2', u'samtools_flagstat', u'samtools_mpileup', u'samtools_phase', u'samtools_rmdup', u'samtools_slice_bam', u'samtools_sort', u'scatterplot', u'show_beginning', u'show_tail', u'sicer', u'snpeff', u'snpfreq', u'split_paired_reads', u'ncbi_sra_toolkit', u'substitution_rates', u'substitutions', u'subtract', u'subtract_query', u'suite_fastx_toolkit_0_0_13', u'suite_samtools_0_1_19', u't2ps', u't2t_report', u'table_annovar', u'table_recalibration', u'tables_arithmetic_operations', u'tabular_to_fasta', u'tabular_to_fastq', u'tophat', u'tophat2', u'tophat_fusion_post', u'trimmer', u't_test_two_samples', u'variant_annotator', u'variant_apply_recalibration', u'variant_combine', u'variant_eval', u'variant_filtration', u'variant_recalibrator', u'variant_select', u'variants_validate', u'varscan_version_2', u'vcf2pgsnp', u'vcf_annotate', u'vcf_extract', u'vcf_filter', u'vcf_intersect', u'vcftools_annotate', u'vcftools_compare', u'vcftools_isec', u'vcftools_merge', u'vcftools_slice', u'vcftools_subset', u'vt_variant_tools', u'weightedaverage', u'windowsplitter', u'xy_plot', u'data_manager_fetch_genome_all_fasta']^M^M

Errored tools (2): [u'suite_gops_1_0', u'suite_samtools_0_1_18']^M^M

All tools listed

In the monitoring  in admin: yellow around the cloning ones?

Can this be fixed? If so how?

Thanks in advance.