notebook.community

Edit and run 





In [89]:



    


import os
import requests



    











In [90]:



    


r = requests.get('https://usegalaxy.org/api/tools')



    











In [91]:



    


usegalaxy_tools = r.json()



    











In [92]:



    


def get_chunks(l, size):
    for i in xrange(0, len(l), size):
        yield l[i: i + size]



    











In [99]:



    


dockerfile = """
# Galaxy - usegalaxy.org clone
#
# VERSION       0.1

FROM bgruening/galaxy-stable:dev

MAINTAINER Bjoern A. Gruening, bjoern.gruening@gmail.com

ENV GALAXY_CONFIG_BRAND usegalaxy.org Clone


"""               

repositories = list()
for section in usegalaxy_tools:
    section_name = section.get('name', '').replace(' ', '_')
    if 'elems' not in section:
        continue
    for tool in section['elems']:
        idd = tool['id']
        if 'toolshed' in idd:
            items = idd.split('/')
            ts = items[0]
            owner = items[2]
            name = items[3]
            repo = '''    "--url https://%s -o %s --name %s --panel-section-name '%s'"''' % (ts, owner, name, section_name)
            repositories.append(repo)

for repos in get_chunks(list(set(repositories)), 10):
    dockerfile += "RUN install-repository \\\n"
    dockerfile += " \\\n".join(repos)
    dockerfile += "\n\n"
with open(os.path.join(os.path.expanduser('~'), 'usegalaxy.Dockerfile'), 'w+') as handle:
    handle.write(dockerfile)
print(dockerfile)



    


















    






# Galaxy - usegalaxy.org clone
#
# VERSION       0.1

FROM bgruening/galaxy-stable:dev

MAINTAINER Bjoern A. Gruening, bjoern.gruening@gmail.com

ENV GALAXY_CONFIG_BRAND usegalaxy.org Clone


RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name subtract_query --panel-section-name 'Join,_Subtract_and_Group'" \
    "--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 table_recalibration --panel-section-name 'NGS:_GATK_Tools_(beta)'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfallelicprimitives --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 filter_transcripts_via_tracking --panel-section-name 'NGS:_RNA-seq'" \
    "--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 devteam --name rcve --panel-section-name 'Regional_Variation'" \
    "--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 tophat_fusion_post --panel-section-name 'NGS:_RNA-seq'"

RUN install-repository \
    "--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 sam_bitwise_flag_filter --panel-section-name 'NGS:_SAMtools'" \
    "--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 devteam --name histogram --panel-section-name 'Graph/Display_Data'" \
    "--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 cluster --panel-section-name 'Operate_on_Genomic_Intervals'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcffixup --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 cuffcompare --panel-section-name 'NGS:_RNA-seq'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name fastqtofasta --panel-section-name 'NGS:_QC_and_manipulation'"

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_quality_converter --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--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 join --panel-section-name 'Operate_on_Genomic_Intervals'" \
    "--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 nick --name allele_counts --panel-section-name 'NGS:_Variant_Analysis'" \
    "--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 short_reads_trim_seq --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 iuc --name stringtie --panel-section-name 'NGS:_RNA-seq'"

RUN install-repository \
    "--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 complement --panel-section-name 'Operate_on_Genomic_Intervals'" \
    "--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 samtools_bedcov --panel-section-name 'NGS:_SAMtools'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfprimers --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfsort --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 gregory-minevich --name bcftools_view --panel-section-name 'NGS:_SAMtools'" \
    "--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 samtools_sort --panel-section-name 'NGS:_SAMtools'"

RUN install-repository \
    "--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 anton --name vcfdistance --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 tabular_to_fastq --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--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 hgv_fundo --panel-section-name 'Phenotype_Association'" \
    "--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 windowsplitter --panel-section-name 'Regional_Variation'" \
    "--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 devteam --name indels_3way --panel-section-name 'Regional_Variation'"

RUN install-repository \
    "--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 vcfleftalign --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 flanking_features --panel-section-name 'Operate_on_Genomic_Intervals'" \
    "--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 ctd_batch --panel-section-name 'Phenotype_Association'" \
    "--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 fastq_filter --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name cuffdiff --panel-section-name 'NGS:_RNA-seq'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfrandomsample --panel-section-name 'NGS:_VCF_Manipulation'"

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 vcf2tsv --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 tyty --name structurefold --panel-section-name 'RNA_Structure_Prediction'" \
    "--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 clustalw --panel-section-name 'Multiple_Alignments'" \
    "--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 dgidb_annotator --panel-section-name 'Phenotype_Association'" \
    "--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 pcingola --name snpeff --panel-section-name 'snpEff'"

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfgeno2haplo --panel-section-name 'NGS:_VCF_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 emboss_5 --panel-section-name 'EMBOSS'" \
    "--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 freebayes_wrapper --panel-section-name 'Phenotype_Association'" \
    "--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 canonical_correlation_analysis --panel-section-name 'Regional_Variation'" \
    "--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 annotation_profiler --panel-section-name 'Operate_on_Genomic_Intervals'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name pileup_parser --panel-section-name 'NGS:_SAMtools'"

RUN install-repository \
    "--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 gregory-minevich --name cloudmap_variant_discovery_mapping --panel-section-name 'NGS:_Variant_Analysis'" \
    "--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 featurecounter --panel-section-name 'Regional_Variation'" \
    "--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 fastq_groomer --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfannotategenotypes --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 fastx_clipper --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'"

RUN install-repository \
    "--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 getindels_2way --panel-section-name 'Regional_Variation'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name fasta_to_tabular --panel-section-name 'Convert_Formats'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfcommonsamples --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 variant_recalibrator --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 plot_from_lda --panel-section-name 'Statistics'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name fastqtofasta --panel-section-name 'Convert_Formats'" \
    "--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 gregory-minevich --name ems_variant_density_mapping --panel-section-name 'NGS:_Variant_Analysis'" \
    "--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 anton --name vcfaddinfo --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 anton --name vcfannotate --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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_trimmer_by_quality --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--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 vcffilter --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name analyze_covariates --panel-section-name 'NGS:_GATK_Tools_(beta)'"

RUN install-repository \
    "--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 bwa_wrappers --panel-section-name 'NGS:_Mapping'" \
    "--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 t2t_report --panel-section-name 'Metagenomic_analyses'" \
    "--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 divide_pg_snp --panel-section-name 'Phenotype_Association'" \
    "--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 fastx_renamer --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name fastq_to_fasta --panel-section-name 'Convert_Formats'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_slice_bam --panel-section-name 'NGS:_SAMtools'"

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfgenotypes --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name quality_filter --panel-section-name 'Regional_Variation'" \
    "--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 microsats_alignment_level --panel-section-name 'Regional_Variation'" \
    "--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 vcfannotate --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 t2ps --panel-section-name 'Metagenomic_analyses'" \
    "--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 samtool_filter2 --panel-section-name 'NGS:_SAMtools'"

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 vcfbreakcreatemulti --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 gregory-minevich --name snp_mapping_using_wgs --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 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 vcfvcfintersect --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 gregory-minevich --name check_snpeff_candidates --panel-section-name 'snpEff'"

RUN install-repository \
    "--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 devteam --name vcfallelicprimitives --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 fasta_concatenate_by_species --panel-section-name 'FASTA_manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfleftalign --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcffilter --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 cuffnorm --panel-section-name 'NGS:_RNA-seq'" \
    "--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 vcfhethom --panel-section-name 'NGS:_VCF_Manipulation'"

RUN install-repository \
    "--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 anton --name vcfhethom --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 anton --name vcfbedintersect --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 principal_component_analysis --panel-section-name 'Regional_Variation'" \
    "--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 vcfgenotypes --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 variants_validate --panel-section-name 'NGS:_GATK_Tools_(beta)'"

RUN install-repository \
    "--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 fastx_reverse_complement --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--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 table_annovar --panel-section-name 'NGS:_Variant_Analysis'" \
    "--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 vcfflatten --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 anton --name vcfcombine --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 bam_to_sam --panel-section-name 'NGS:_SAMtools'"

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 fastx_artifacts_filter --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--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 anton --name vcfvcfintersect --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 devteam --name short_reads_figure_score --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 correlation --panel-section-name 'Statistics'" \
    "--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 column_maker --panel-section-name 'Text_Manipulation'"

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name substitutions --panel-section-name 'Regional_Variation'" \
    "--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 vcfcombine --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfcheck --panel-section-name 'NGS:_VCF_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 fastq_stats --panel-section-name 'NGS:_QC_and_manipulation'" \
    "--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 fastx_collapser --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 samtools_reheader --panel-section-name 'NGS:_SAMtools'"

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 mutate_snp_codon --panel-section-name 'Evolution'" \
    "--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 subtract --panel-section-name 'Operate_on_Genomic_Intervals'" \
    "--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 anton --name vcf2tsv --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--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 kernel_principal_component_analysis --panel-section-name 'Regional_Variation'" \
    "--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 fastq_to_fasta --panel-section-name 'NGS:_QC_and_manipulation'"

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 variant_filtration --panel-section-name 'NGS:_GATK_Tools_(beta)'" \
    "--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 intersect --panel-section-name 'Operate_on_Genomic_Intervals'" \
    "--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 merge --panel-section-name 'Operate_on_Genomic_Intervals'" \
    "--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 cuffmerge --panel-section-name 'NGS:_RNA-seq'" \
    "--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 samtools_flagstat --panel-section-name 'NGS:_SAMtools'"

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name dna_filtering --panel-section-name 'Filter_and_Sort'" \
    "--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 generate_pc_lda_matrix --panel-section-name 'Statistics'" \
    "--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 blankenberg --name naive_variant_caller --panel-section-name 'NGS:_Variant_Analysis'" \
    "--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 logistic_regression_vif --panel-section-name 'Regional_Variation'" \
    "--url https://toolshed.g2.bx.psu.edu -o devteam --name samtools_split --panel-section-name 'NGS:_SAMtools'" \
    "--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 tabular_to_fasta --panel-section-name 'Convert_Formats'"

RUN install-repository \
    "--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 find_diag_hits --panel-section-name 'Metagenomic_analyses'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfselectsamples --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 devteam --name vcftools_slice --panel-section-name 'NGS:_Variant_Analysis'" \
    "--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 microsats_mutability --panel-section-name 'Regional_Variation'" \
    "--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 vcfrandomsample --panel-section-name 'NGS:_VCF_Manipulation'" \
    "--url https://toolshed.g2.bx.psu.edu -o anton --name vcfbreakcreatemulti --panel-section-name 'NGS:_VCF_Manipulation'"

RUN install-repository \
    "--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 guru-ananda --name karyotype_plot --panel-section-name 'Regional_Variation'"



















In [ ]:

Content source: mvdbeek/notebooks

Similar notebooks:

notebook.community | gallery | about