HISTORY.rst
LICENSE
Makefile
README.rst
dev-requirements.txt
mypy.ini
pyproject.toml
pytest.ini
setup.cfg
scripts/commit_version.py
scripts/new_version.py
scripts/print_version_for_release.py
src/galaxy/config/__init__.py
src/galaxy/config/chat_prompts.json
src/galaxy/config/config_manage.py
src/galaxy/config/py.typed
src/galaxy/config/schema.py
src/galaxy/config/script.py
src/galaxy/config/templates.py
src/galaxy/config/url_headers.py
src/galaxy/config/sample/agent_model_capabilities.yml.sample
src/galaxy/config/sample/auth_conf.xml.sample
src/galaxy/config/sample/build_sites.yml.sample
src/galaxy/config/sample/container_resolvers.yml.sample
src/galaxy/config/sample/data_manager_conf.xml.sample
src/galaxy/config/sample/datatypes_conf.xml.sample
src/galaxy/config/sample/disposable_email_blocklist.conf.sample
src/galaxy/config/sample/environment_modules_mapping.yml.sample
src/galaxy/config/sample/error_report.yml.sample
src/galaxy/config/sample/file_sources_conf.yml.sample
src/galaxy/config/sample/galaxy.yml.sample
src/galaxy/config/sample/job_conf.sample.yml
src/galaxy/config/sample/job_conf.xml.sample_advanced
src/galaxy/config/sample/job_conf.xml.sample_basic
src/galaxy/config/sample/job_resource_params_conf.xml.sample
src/galaxy/config/sample/lmod_modules_mapping.yml.sample
src/galaxy/config/sample/local_conda_mapping.yml.sample
src/galaxy/config/sample/object_store_conf.sample.yml
src/galaxy/config/sample/object_store_conf.xml.sample
src/galaxy/config/sample/oidc_backends_config.xml.sample
src/galaxy/config/sample/oidc_config.xml.sample
src/galaxy/config/sample/reports.yml.sample
src/galaxy/config/sample/themes_conf.yml.sample
src/galaxy/config/sample/tool_conf.xml.sample
src/galaxy/config/sample/tool_data_table_conf.xml.sample
src/galaxy/config/sample/tool_destinations.yml.sample
src/galaxy/config/sample/tool_recommendations_overwrite.yml.sample
src/galaxy/config/sample/tool_shed.yml.sample
src/galaxy/config/sample/tool_sheds_conf.xml.sample
src/galaxy/config/sample/trs_servers_conf.yml.sample
src/galaxy/config/sample/url_headers_conf.yml.sample
src/galaxy/config/sample/user_preferences_extra_conf.yml.sample
src/galaxy/config/sample/workflow_resource_mapper_conf.yml.sample
src/galaxy/config/sample/workflow_resource_params_conf.xml.sample
src/galaxy/config/sample/workflow_schedulers_conf.xml.sample
src/galaxy/config/schemas/config_schema.yml
src/galaxy/config/schemas/job_config_schema.yml
src/galaxy/config/schemas/reports_config_schema.yml
src/galaxy/config/schemas/tool_shed_config_schema.yml
src/galaxy/config/templates/mail/activation-email.html
src/galaxy/config/templates/mail/activation-email.txt
src/galaxy/config/templates/mail/notifications/message-email.html
src/galaxy/config/templates/mail/notifications/message-email.txt
src/galaxy/config/templates/mail/notifications/new_shared_item-email.html
src/galaxy/config/templates/mail/notifications/new_shared_item-email.txt
src/galaxy/config/templates/mail/notifications/storage_operation-email.html
src/galaxy/config/templates/mail/notifications/storage_operation-email.txt
src/galaxy_config.egg-info/PKG-INFO
src/galaxy_config.egg-info/SOURCES.txt
src/galaxy_config.egg-info/dependency_links.txt
src/galaxy_config.egg-info/entry_points.txt
src/galaxy_config.egg-info/requires.txt
src/galaxy_config.egg-info/top_level.txt
test-data/1.RData
test-data/1.axt
test-data/1.bam
test-data/1.bed
test-data/1.bed.spaces
test-data/1.bedgraph
test-data/1.bigbed
test-data/1.bigwig
test-data/1.csv
test-data/1.ct
test-data/1.customtrack
test-data/1.fasta
test-data/1.fasta.gz
test-data/1.fastq
test-data/1.fastqsanger
test-data/1.fastqsanger.bz2
test-data/1.fastqsanger.gz
test-data/1.fastqsolexa
test-data/1.interval
test-data/1.lav
test-data/1.pileup
test-data/1.sam
test-data/1.sam.gz
test-data/1.scf
test-data/1.sff
test-data/1.tabular
test-data/1.tiff
test-data/1.txt
test-data/1.wig
test-data/1.yaml
test-data/11.tabular
test-data/2.bed
test-data/2.cram
test-data/2.csv
test-data/2.fasta
test-data/2.tabular
test-data/2gen.fastq
test-data/3.bam
test-data/3.bed
test-data/3.maf
test-data/3unsorted.bam
test-data/4.bed
test-data/4.bed.bz2
test-data/4.bed.gz
test-data/4.bed.zip
test-data/454Score.pdf
test-data/454Score.png
test-data/5.bed
test-data/5.gff
test-data/5.gff3
test-data/5_Ig-like.gff
test-data/6.bed
test-data/7.bed
test-data/8.bed
test-data/9.bed
test-data/GRCm38mm10_chr5_34761740-34912521.fa
test-data/MTBLS6.zip
test-data/a.tab
test-data/a.txt
test-data/asian_chars_1.txt
test-data/bad.html.gz
test-data/bam_from_sam.bam
test-data/bam_native_from_sam.bam
test-data/bcf_index_metadata_test.bcf
test-data/bcf_index_metadata_test.txt
test-data/biom1_metadata_test.txt
test-data/chebi_57262.v3k.mol
test-data/chopper.h5
test-data/composite_output_expected_log
test-data/drugbank_drugs.cml
test-data/drugbank_drugs.inchi
test-data/drugbank_drugs.mol
test-data/drugbank_drugs.mol2
test-data/drugbank_drugs.sdf
test-data/drugbank_drugs.smi
test-data/empty.txt
test-data/example-bag.zip
test-data/filter1_in3.sam
test-data/filter1_in5.tab
test-data/filter1_in6.bed
test-data/filter1_inbad.bed
test-data/filter1_test1.bed
test-data/filter1_test2.bed
test-data/filter1_test3.sam
test-data/filter1_test4.bed
test-data/filter1_test5.tab
test-data/filter1_test6.bed
test-data/filter_labels_1.txt
test-data/html_file.txt
test-data/im1_uint8.png
test-data/im1_uint8.tif
test-data/im2_a.png
test-data/im2_b.png
test-data/im3_a.png
test-data/im3_b.tif
test-data/im3_b_bool.tiff
test-data/im4_float.tif
test-data/im5_uint8.tif
test-data/im6_uint8.tif
test-data/im7_uint8.tif
test-data/im8_uint16.tif
test-data/im9_multiseries.tif
test-data/im_empty.tif
test-data/input_taxonomy.biom1
test-data/joiner_header_in1.tab
test-data/joiner_header_in2.tab
test-data/joiner_out1.bed
test-data/joiner_out2.bed
test-data/joiner_out3.bed
test-data/joiner_out4.bed
test-data/joiner_out5.tab
test-data/joiner_out6.tab
test-data/joiner_out7.tab
test-data/matrix.cool
test-data/neostore.zip
test-data/new_element_sort_order.txt
test-data/new_labels_1.txt
test-data/new_labels_2.txt
test-data/new_labels_3.txt
test-data/new_labels_bad_1.txt
test-data/new_labels_bad_2.txt
test-data/new_tags_1.txt
test-data/phiX.fasta
test-data/qname_sorted.bam
test-data/qualscores.qual454
test-data/qualscores.qualsolid
test-data/random-file
test-data/rgenetics.bed
test-data/rgenetics.bim
test-data/rgenetics.fam
test-data/rgenetics.map
test-data/rgenetics.ped
test-data/rocrate-test.zip
test-data/safe_relative_symlink.tar
test-data/safetar_with_symlink.tar
test-data/sam_with_header.sam
test-data/selenium-test-notebook.ipynb
test-data/shrimp_cs_test1.csfasta
test-data/simple.xml
test-data/simple_line.txt
test-data/simple_line_alternative.txt
test-data/simple_line_no_newline.txt
test-data/simple_line_x2.txt
test-data/simple_line_x2_windows.txt
test-data/simple_line_x3.txt
test-data/simple_line_x5.txt
test-data/simple_lines_both.txt
test-data/simple_lines_interleaved.txt
test-data/sort_out1.bed
test-data/sort_out2.bed
test-data/sort_out3.tab
test-data/sort_out4.sam
test-data/test.vcf
test-data/test.vcf.gz
test-data/testdir.tar
test-data/testdir1.tar
test-data/testdir1.tar.gz
test-data/testdir1.zip
test-data/tinywga.bed
test-data/tinywga.bim
test-data/tinywga.fam
test-data/tinywga.map
test-data/tinywga.ped
test-data/tinywga.ped.space_to_tab
test-data/unsafe.tar
test-data/unsafe.zip
test-data/unsafe_relative_symlink.tar
test-data/bwa_mem2_index/1.fasta
test-data/exports/1901_two_datasets.tgz
test-data/highdicom/LICENSE
test-data/highdicom/ct_image.dcm
test-data/highdicom/seg_image_ct_binary.dcm
test-data/highdicom/sm_image.dcm
test-data/library/3.bed
test-data/library/4.bed
test-data/library/5.bed
test-data/rules/PRJDA60709.tsv
test-data/rules/PRJDB3920.tsv
test-data/rules/PRJNA355367.tsv
test-data/rules/treated1fb.txt
test-data/rules/treated2fb.txt
test-data/rules/treated3fb.txt
test-data/rules/uniprot.json
test-data/rules/uniprot.tsv
test-data/rules/untreated1fb.txt
test-data/rules/untreated2fb.txt
test-data/rules/untreated3fb.txt
test-data/rules/untreated4fb.txt
test-data/users/test1@bx.psu.edu/1.fasta
test-data/users/test3@bx.psu.edu/run1/2.fasta
tests/__init__.py
tests/config/__init__.py
tests/config/test_config_dataset_storage.py
tests/config/test_config_values.py
tests/config/test_load_config.py
tests/config/test_path_graph.py
tests/config/test_path_resolves_to.py
tests/config/test_reload_config.py
tests/config/test_schema.py
tests/config/config_manage/__init__.py
tests/config/config_manage/test_config_manage.py
tests/config/config_manage/1607_root_filters/config/galaxy.ini
tests/config/config_manage/1607_root_filters/config/tool_shed.ini
tests/config/config_manage/1607_root_samples/config/galaxy.ini
tests/config/config_manage/1607_root_samples/config/reports.ini
tests/config/config_manage/1607_root_samples/config/tool_shed.ini
tests/config/config_manage/1705_allow_path_paste/config/galaxy.ini
tests/config/config_manage/embedded/config/galaxy.yml
tests/config/config_manage/simple/config/galaxy.yml