HISTORY.rst
LICENSE
MANIFEST.in
Makefile
README.rst
dev-requirements.txt
requirements.txt
setup.cfg
setup.py
test-requirements.txt
galaxy/__init__.py
galaxy/project_galaxy_util.py
galaxy/exceptions/__init__.py
galaxy/exceptions/error_codes.json
galaxy/exceptions/error_codes.py
galaxy/util/__init__.py
galaxy/util/aliaspickler.py
galaxy/util/bunch.py
galaxy/util/bytesize.py
galaxy/util/checkers.py
galaxy/util/commands.py
galaxy/util/compression_utils.py
galaxy/util/dbkeys.py
galaxy/util/dictifiable.py
galaxy/util/docutils_template.txt
galaxy/util/expressions.py
galaxy/util/facts.py
galaxy/util/filelock.py
galaxy/util/form_builder.py
galaxy/util/getargspec.py
galaxy/util/hash_util.py
galaxy/util/heartbeat.py
galaxy/util/image_util.py
galaxy/util/inflection.py
galaxy/util/json.py
galaxy/util/jstree.py
galaxy/util/lazy_process.py
galaxy/util/monitors.py
galaxy/util/object_wrapper.py
galaxy/util/odict.py
galaxy/util/oset.py
galaxy/util/permutations.py
galaxy/util/plugin_config.py
galaxy/util/properties.py
galaxy/util/renamed_temporary_file.py
galaxy/util/rules_dsl.py
galaxy/util/rules_dsl_spec.yml
galaxy/util/sanitize_html.py
galaxy/util/script.py
galaxy/util/search.py
galaxy/util/simplegraph.py
galaxy/util/sleeper.py
galaxy/util/sockets.py
galaxy/util/specs.py
galaxy/util/sqlite.py
galaxy/util/submodules.py
galaxy/util/template.py
galaxy/util/tool_version.py
galaxy/util/topsort.py
galaxy/util/ucsc.py
galaxy/util/validation.py
galaxy/util/watcher.py
galaxy/util/web_compat.py
galaxy/util/xml_macros.py
galaxy/util/yaml_util.py
galaxy/util/zipstream.py
galaxy/util/custom_logging/__init__.py
galaxy/util/custom_logging/fluent_log.py
galaxy/util/pastescript/__init__.py
galaxy/util/pastescript/loadwsgi.py
galaxy/util/pastescript/serve.py
galaxy/util/path/__init__.py
galaxy/util/path/ntpath.py
galaxy/util/path/posixpath.py
galaxy/util/tool_shed/__init__.py
galaxy/util/tool_shed/common_util.py
galaxy/util/tool_shed/encoding_util.py
galaxy/util/tool_shed/xml_util.py
galaxy_util.egg-info/PKG-INFO
galaxy_util.egg-info/SOURCES.txt
galaxy_util.egg-info/dependency_links.txt
galaxy_util.egg-info/entry_points.txt
galaxy_util.egg-info/not-zip-safe
galaxy_util.egg-info/requires.txt
galaxy_util.egg-info/top_level.txt
scripts/commit_version.py
scripts/new_version.py
scripts/print_version_for_release.py
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.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/11.tabular
test-data/2.bed
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/cat_wrapper_out1.bed
test-data/composite_output_expected_log
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/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_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/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_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/exports/1901_two_datasets.tgz
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/util/test_checkers.py
tests/util/test_compression_util.py
tests/util/test_fill_template.py
tests/util/test_fix_type_error.py
tests/util/test_get_url.py
tests/util/test_inflection.py
tests/util/test_lazy_process.py
tests/util/test_properties.py
tests/util/test_rule_utils.py
tests/util/test_sockets.py
tests/util/test_sqlite_utils.py
tests/util/test_topsort.py
tests/util/test_utils.py