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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

Failed: Bad Request (400) by uploading #99

Closed mictadlo closed 8 years ago

mictadlo commented 8 years ago

Hello, I tried to upload a VCF file (3.7 MB) which has caused Failed: Bad Request (400) with the following Dockerfile:

FROM bgruening/galaxy-stable:dev
MAINTAINER auto script
ENV GALAXY_CONFIG_BRAND CARF
ENV GALAXY_CONFIG_SERVE_XSS_VULNERABLE_MIMETYPES ChemicalToolBox
ENV GALAXY_CONFIG_ENABLE_BETA_TOOL_COMMAND_ISOLATION True

WORKDIR /galaxy-central

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 pileup_parser --panel-section-name NGS:_SAMtools" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name t2ps --panel-section-name Metagenomic_analyses" \
    "--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 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 fastq_to_tabular --panel-section-name NGS:_QC_and_manipulation" \
    "--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 concat --panel-section-name Operate_on_Genomic_Intervals"

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 vcf2pgsnp --panel-section-name Phenotype_Association" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name column_maker --panel-section-id textutil" \
    "--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 principal_component_analysis --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name weblogo3 --panel-section-name Motif_Tools"

RUN install-repository \
    "--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 lda_analysis --panel-section-name Statistics" \
    "--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 bamtools_filter --panel-section-name NGS:_BAM_Tools" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffmerge --panel-section-name NGS:_RNA-seq" \
    "--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"

RUN install-repository \
    "--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 merge --panel-section-name Operate_on_Genomic_Intervals" \
    "--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 miller-lab --name genome_diversity --panel-section-name Genome_Diversity" \
    "--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 find_diag_hits --panel-section-name Metagenomic_analyses" \
    "--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 cuffdiff --panel-section-name NGS:_RNA-seq"

RUN install-repository \
    "--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 kernel_canonical_correlation_analysis --panel-section-name Regional_Variation" \
    "--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 best_regression_subsets --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o tyty --name structurefold --panel-section-name RNA_Structure_Prediction" \
    "--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 fastqc --panel-section-name NGS:_QC_and_manipulation" \
    "--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 bam_to_sam --panel-section-name NGS:_SAMtools"

RUN install-repository \
    "--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 bamtools_split --panel-section-name NGS:_BAM_Tools" \
    "--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 fastx_collapser --panel-section-name FASTA_manipulation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name gi2taxonomy --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_reheader --panel-section-name NGS:_SAMtools" \
    "--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 kernel_principal_component_analysis --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name unified_genotyper --panel-section-name NGS:_GATK_Tools_(beta)"

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffquant --panel-section-name NGS:_RNA-seq" \
    "--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 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" \
    "--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 devteam --name logistic_regression_vif --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name macs --panel-section-name NGS:_Peak_Calling"

RUN install-repository \
    "--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 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" \
    "--url https://toolshed.g2.bx.psu.edu -o gregory-minevich --name cloudmap_variant_discovery_mapping --panel-section-name NGS:_Variant_Analysis" \
    "--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 partialr_square --panel-section-name Regional_Variation" \
    "--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 poisson2test --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffcompare --panel-section-name NGS:_RNA-seq"

RUN install-repository \
    "--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 devteam --name vcfcheck --panel-section-name NGS:_VCF_Manipulation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name substitutions --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o gregory-minevich --name cloudmap_in_silico_complementation --panel-section-name NGS:_Variant_Analysis" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name rcve --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffnorm --panel-section-name NGS:_RNA-seq" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name variants_validate --panel-section-name NGS:_GATK_Tools_(beta)" \
    "--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"

RUN install-repository \
    "--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 freebayes_wrapper --panel-section-name Phenotype_Association" \
    "--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 devteam --name indels_3way --panel-section-name Regional_Variation" \
    "--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 picard --panel-section-name NGS:_Picard_(beta)" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_apply_recalibration --panel-section-name NGS:_GATK_Tools_(beta)"

RUN install-repository \
    "--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 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 fastqtofasta --panel-section-name NGS:_QC_and_manipulation" \
    "--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" \
    "--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 gregory-minevich --name ems_variant_density_mapping --panel-section-name NGS:_Variant_Analysis" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_sort --panel-section-name NGS:_SAMtools"

RUN install-repository \
    "--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" \
    "--url https://toolshed.g2.bx.psu.edu -o iuc --name stringtie --panel-section-name NGS:_RNA-seq" \
    "--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 guru-ananda --name rhmm --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name variant_annotator --panel-section-name NGS:_GATK_Tools_(beta)"

RUN install-repository \
    "--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 devteam --name cluster --panel-section-name Operate_on_Genomic_Intervals" \
    "--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 fastq_to_fasta --panel-section-name NGS:_QC_and_manipulation" \
    "--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 boris --name phylorelatives --panel-section-name NGS:_Variant_Analysis" \
    "--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 devteam --name microsats_alignment_level --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o guru-ananda --name heatmap --panel-section-name Regional_Variation"

RUN install-repository \
    "--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 devteam --name bamtools --panel-section-name NGS:_BAM_Tools" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name dna_filtering --panel-section-id filter" \
    "--url https://toolshed.g2.bx.psu.edu -o blankenberg --name naive_variant_caller --panel-section-name NGS:_Variant_Analysis" \
    "--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 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"

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name tophat_fusion_post --panel-section-name NGS:_RNA-seq" \
    "--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 mutate_snp_codon --panel-section-name Evolution" \
    "--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 gffread --panel-section-name NGS:_RNA-seq" \
    "--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 devteam --name linear_regression --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name varscan_version_2 --panel-section-name NGS:_Variant_Analysis" \
    "--url https://toolshed.g2.bx.psu.edu -o pcingola --name snpeff --panel-section-name snpEff"

RUN install-repository \
    "--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 generate_pc_lda_matrix --panel-section-name Statistics" \
    "--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 clustalw --panel-section-name Multiple_Alignments" \
    "--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" \
    "--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 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"

RUN install-repository \
    "--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 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 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 devteam --name cufflinks --panel-section-name NGS:_RNA-seq" \
    "--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 t2t_report --panel-section-name Metagenomic_analyses" \
    "--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 gregory-minevich --name check_snpeff_candidates --panel-section-name snpEff"

RUN install-repository \
    "--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 devteam --name table_annovar --panel-section-name NGS:_Variant_Analysis" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name canonical_correlation_analysis --panel-section-name Regional_Variation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name filter_transcripts_via_tracking --panel-section-name NGS:_RNA-seq" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfbreakcreatemulti --panel-section-name NGS:_VCF_Manipulation" \
    "--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 join --panel-section-name Operate_on_Genomic_Intervals" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name lca_wrapper --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfannotate --panel-section-name NGS:_VCF_Manipulation"

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfrandomsample --panel-section-name NGS:_VCF_Manipulation" \
    "--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 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 tabular_to_fastq --panel-section-name NGS:_QC_and_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 devteam --name fastx_clipper --panel-section-name NGS:_QC_and_manipulation" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name tophat2 --panel-section-name NGS:_RNA-seq" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name vcfcommonsamples --panel-section-name NGS:_VCF_Manipulation" \
   #double#"--url https://toolshed.g2.bx.psu.edu -o devteam --name fastx_collapser --panel-section-name NGS:_QC_and_manipulation"

RUN install-repository \
    "--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 sam_to_bam --panel-section-name NGS:_SAMtools" \
    "--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 gregory-minevich --name snp_mapping_using_wgs --panel-section-name NGS:_Variant_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 fastq_combiner --panel-section-name NGS:_QC_and_manipulation" \
    "--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" \
    "--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 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"
RUN install-repository "--url https://toolshed.g2.bx.psu.edu/ -o anmoljh --name trinityrnaseq --panel-section-name Assembly"
RUN install-repository "--url https://toolshed.g2.bx.psu.edu/ -o anmoljh --name trinitystats --panel-section-name Assembly"
RUN install-repository "--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

RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update && \
    apt-get install --no-install-recommends -y wget libcairo2-dev && \
    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# 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://toolshed.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://toolshed.g2.bx.psu.edu/ -o bgruening --name package_openms_latest"
RUN install-repository "--url https://toolshed.g2.bx.psu.edu/ -o galaxyp --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 package_blast_plus_2_2_29" \
    "--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" 

RUN install-repository \
    "--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 install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name clinod --panel-section-name Localisation" \
    "--url https://toolshed.g2.bx.psu.edu/ -o vipints --name nupop_0.1 --panel-section-name Localisation" \
    "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name twistdna --panel-section-name DNAStructure" \
    "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name repeat_masker --panel-section-name DNAStructure" \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name effectivet3 --panel-section-name Classification" \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name nlstradamus --panel-section-name Classification"

# FASTA tools
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o galaxyp --name fasta_merge_files_and_filter_unique_sequences --panel-section-name FASTA_manipulation" \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name seq_filter_by_id --panel-section-name FASTA_manipulation" \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name seq_rename --panel-section-name FASTA_manipulation" \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name seq_select_by_id --panel-section-name FASTA_manipulation" \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name get_orfs_or_cdss --panel-section-name FASTA_manipulation" \
    "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name find_subsequences --panel-section-name FASTA_manipulation" 

# Plotting

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name venn_list --panel-section-name Plotting" \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name mummer --panel-section-name Plotting" \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name jbrowse --panel-section-name Plotting"

# Assembly tools
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o lionelguy --name spades --panel-section-name Plotting" \
    "--url https://toolshed.g2.bx.psu.edu/ -o peterjc --name mira4_assembler --panel-section-name Plotting"

## Install ChiP-seq
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o kevyin --name homer --panel-section-name NGS:_Peak_Calling" \
#    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_homer_4_2 --panel-section-name NGS:_Peak_Calling" \
    "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name ccat --panel-section-name NGS:_Peak_Calling" \
    "--url https://toolshed.g2.bx.psu.edu/ -o modencode-dcc --name idr_package --panel-section-name NGS:_Peak_Calling" \
    "--url https://toolshed.g2.bx.psu.edu/ -o pjbriggs --name ceas --panel-section-name NGS:_Peak_Calling" \
    "--url https://toolshed.g2.bx.psu.edu/ -o pjbriggs --name weeder2 --panel-section-name NGS:_Peak_Calling" \
    "--url https://toolshed.g2.bx.psu.edu/ -o ngsplot --name ngsplot --panel-section-name NGS:_Peak_Calling"

## Metagenomic
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o azuzolo --name qiime1_3_0 --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name usearch_cluster_otus --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name usearch_dereplication --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name usearch_map_reads_to_otus --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name usearch_uchime --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name rdp_multiclassifier --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name pynast --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name fasttree_linux_64bit --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name rarefaction --panel-section-name Metagenomic_analyses" \ 
    "--url https://toolshed.g2.bx.psu.edu -o qfab --name collector_curve --panel-section-name Metagenomic_analyses" \
    "--url https://toolshed.g2.bx.psu.edu -o fangly --name copyrighter --panel-section-name Metagenomic_analyses"

## Community workflows
#RUN install-repository \
#    "--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name package_galaxy_ops_1_0_0" \
#    "--url https://testtoolshed.g2.bx.psu.edu/ -o bgruening --name glimmer_gene_calling_workflow" \ 
#    "--url https://testtoolshed.g2.bx.psu.edu/ -o bgruening --name find_genes_located_nearby_workflow" \
#    "--url https://testtoolshed.g2.bx.psu.edu/ -o bgruening --name find_three_genes_located_nearby_workflow" \
#   "--url https://testtoolshed.g2.bx.psu.edu/ -o peterjc --name secreted_protein_workflow" \
#   "--url https://testtoolshed.g2.bx.psu.edu/ -o peterjc --name rxlr_venn_workflow"

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 ppa:nebc/bio-linux && \
    apt-get update && \
    apt-get install -y  meme=1:4.10.0.1-0ubuntu2  && \
    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ADD tool_conf.xml config/

# package_matplotlib_1_2

# Mark folders as imported from the host.
VOLUME ["/export/", "/data/", "/var/lib/docker"]

# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9001 (Galaxy report app),
#8000 (SimpleHTTPServer), 9002 (supervisor webui)
EXPOSE :80
EXPOSE :21
EXPOSE :5432
EXPOSE :8000
EXPOSE :8800
EXPOSE :9001
EXPOSE :9002

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

What did I do wrong?

Thank you in advance.

Mic

bgruening commented 8 years ago

I would need an error message to tell you more ...

mictadlo commented 8 years ago

Hi @bgruening, I changed to bgruening/galaxy-stable:15.07 and the error massage changed to Failed: Not Found (404) while uploading a local file through the of upload/dowload icon on the left top side.

The Galaxy container is also missing Get Data heading on the left and e.g. the below tools are not there:

Which information do you require and where are there located.

Update: Chrome console has shown the following error: Name: _upload Status: 404 Type: xhr Initiator: uploadbox.js:278 Size: 373B

Thank you in advance.

Mic

mictadlo commented 8 years ago

Udate2: Is this (http://gmod.827538.n3.nabble.com/Data-uploaded-with-new-upload-tool-doesn-t-get-added-to-history-td4046375.html) maybe the solution?

bgruening commented 8 years ago

I would need the Galaxy log file? I guess that Slurm is not running. Can you upload any file? Start any job? We have added extensive testing in the :dev branch, that also tests uploading files. With this you can see immediately, if you container works or not.

bgruening commented 8 years ago

@mictadlo we added a large test suite into the dev branch and are now testing all images with bioblend. So we are uploading data, running tools and so on. I hope this is working now for you as well.