MetaPathways/.gitignore at dev · hallamlab/MetaPathways · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
*.sif
*.pyc
*.swp
.idea*
*.DS_Store
redhat
rpkm_c
*.o
binaries/*/*
*.pyc
*.swp
.idea*
*.DS_Store
*.o
.snakemake
.tox
coverage.xml
pathologic.log
*.sif
\#*
*pathway-tools-*-install
__pycache__

test
extensions/FAST/fastal
extensions/FAST/fastdb
extensions/metacount/metacount
extensions/FAST/src/*.o
extensions/FAST/gumbel_params/*
extensions/metacount/parser/libbamparser.a
.snakemake

Metapathways_DBs_2016-04.tar.xz
MetaPathways_DBs
config/template_config.txt
config/template_param.txt

dist
docker/dist
src/MetaPathways.egg-info/*
MetaPathways.egg-info
metapathways.egg-info

build
docs/_build/*
docs/_templates/*
docs/_static/*
docs/_build/*/*
docs/_templates/*/*
docs/_static/*/*
*~

workflows/.snakemake
workflows/logs
workflows/SRA_download
workflows/SRA_fastq
workflows/SRA_gz

/conda_build
/conda_recipe/*
!/conda_recipe/compile_recipe.py
!/conda_recipe/meta_template.yaml
global_errors_warnings.txt

.vscode

# Local environments and generated validation/build products
/venv/
/.venv/
/regtests/output/
/tests/data/output/
/metapathways/tests/data/output/
/tests/data/lagoon-sample/output/
/metapathways/regtests/test_db/functional/formatted/
/metapathways/regtests/test_db/taxonomic/formatted/
/metapathways/regtests/test_db/functional_categories/
/metapathways/regtests/test_db/ncbi_tree/
/metapathways/regtests/test_db/starting_build
/metapathways/regtests/test_db/temp_cache/
/docs/build/
*.a
*.so
# SAM/BAM and sequence/archive formats are intentionally not ignored globally:
# the native parser tests and regression fixtures contain legitimate examples.

# Local manuscript figures and their export tools
/docs/figures/