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re-adding bioconda install instructions #7

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re-adding bioconda install instructions #7

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630eadd
demo notebook update, config update, tests update
crohlicek Dec 1, 2023
0655639
PR updates to demo notebook
crohlicek Dec 2, 2023
db7154f
Merge pull request #3 from PopicLab/config_updates
crohlicek Dec 2, 2023
3902e56
move wiki to git (#1)
notestaff Dec 2, 2023
022e29a
removing install/ dir for now, obsoleted by pip install (#2)
notestaff Dec 2, 2023
5a8850d
.gitignore: added notebook outputs
notestaff Dec 2, 2023
9f6dde0
update version to 0.0.5
notestaff Dec 2, 2023
211967e
move license to pyproject.toml
notestaff Dec 2, 2023
dc71730
demo notebook fixes
notestaff Dec 2, 2023
09d18c9
adding demo notebook conda env definition
notestaff Dec 2, 2023
91b5cb6
change pbsim3 model path
notestaff Dec 2, 2023
af36d77
insilicosv-demo-env: added minimap2
notestaff Dec 2, 2023
d82a5c1
use pbsim3 model from the pbsim3 conda package
notestaff Dec 2, 2023
9c8de97
added igv to demo notebook conda env
notestaff Dec 2, 2023
bbae983
made simulated read coverage configurable in demo notebook via env vars
notestaff Dec 2, 2023
6096c40
update demo notebook env to current igv
notestaff Dec 2, 2023
8965bf6
fix env name
notestaff Dec 2, 2023
51573e1
.gitignore: add IGV_screenshots
notestaff Dec 2, 2023
62b060e
adding the original definition of insilicosv-demo-env
notestaff Dec 4, 2023
d9d494c
.gitignore: added workflow-related ignores
notestaff Dec 6, 2023
dc4303c
docs: README.md install instructions changed to use pip or bioconda
notestaff Dec 6, 2023
ae69e8e
fixed gitignore
notestaff Dec 6, 2023
e2f29c5
change references to simulate.py into references to insilicosv execut…
notestaff Dec 6, 2023
9933b38
Merge pull request #4 from PopicLab/is-231202-1406-add-demo-env
crohlicek Dec 6, 2023
1fe8da0
Merge pull request #5 from PopicLab/is-231206-1130-docs-fix-install-i…
crohlicek Dec 6, 2023
7c2b270
added demo notebook instructions
notestaff Dec 6, 2023
286d887
docs: README.md -- clarified where to find config file syntax
notestaff Dec 6, 2023
2e3e2eb
fixed image link for the grammar
notestaff Dec 6, 2023
328ddcb
added space around image ref
notestaff Dec 6, 2023
aebc8f9
added more spaces around image refs to ensure correct display on github
notestaff Dec 6, 2023
6d4c1f6
removed divergent repeat example visualization
notestaff Dec 6, 2023
419cb1e
README updates (directory setup for user)
crohlicek Dec 6, 2023
117834e
Merge pull request #6 from PopicLab/documentation_updates
crohlicek Dec 6, 2023
de194fd
removed, for now, documentation reference to the utility code that ma…
notestaff Dec 6, 2023
301576f
removed get_original_base_pos() from utils.py for now
notestaff Dec 6, 2023
8a73189
removed div_repeat_postproc
notestaff Dec 6, 2023
55edb3f
Catchup current changes (#7)
notestaff Dec 6, 2023
e08eddc
removed whitespace
notestaff Dec 6, 2023
a090bd0
Example use case updates (#8)
crohlicek Dec 8, 2023
bb25e6d
Output bed update (#9)
crohlicek Dec 8, 2023
d141bab
Config structure change (#10)
crohlicek Dec 8, 2023
22c3f85
updates / typo corrections to demo notebook markdown cells (#13)
crohlicek Dec 8, 2023
e9923bb
Minor edits to input_guidelines.md
crohlicek Dec 8, 2023
87181fb
removed unit test for base mapping util not included in this release
crohlicek Dec 8, 2023
6ccd8b2
Merge branch 'develop' of https://github.com/PopicLab/insilicoSV-dev …
crohlicek Dec 8, 2023
1df98f5
changed version to 0.0.6
notestaff Dec 8, 2023
f4df4e5
removed the linux-specific env definition workflows/insilicosv-demo-e…
notestaff Dec 8, 2023
a02af25
Adjust install instructions for the period while pip has the current …
notestaff Dec 8, 2023
7513df7
install instructions: use pip install --upgrade
notestaff Dec 8, 2023
da5d465
Merge remote-tracking branch 'origin-pub/main' into develop
notestaff Dec 8, 2023
81678fa
demo notebook docs: added M1 Mac install instructions
notestaff Dec 8, 2023
cf62a8e
Merge remote-tracking branch 'origin-pub/main' into develop
notestaff Dec 12, 2023
099454b
re-adding conda install instructions
notestaff Dec 12, 2023
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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,10 @@ Installation using pip:

* `$ pip install insilicosv`

<!-- Installation using conda:
Installation using conda:

* Install and configure [bioconda](https://bioconda.github.io/)
* Install insilicosv with `conda install insilicosv` -->
* Install insilicosv with `conda install insilicosv`

## To Run
The recommended workflow for running insilicoSV is as follows:
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