Adding DifCover to bioconda

[nikostr]

Hi! Thanks for this tool! I just wanted to let you know that I've created a PR to make DifCover installable through bioconda (bioconda/bioconda-recipes#48098). My reason for doing this is that it will make it easier to integrate DifCover scripts into snakemake pipelines and wrappers, but I hope it might be useful for others as well.

[timnat]

Thank you nikostr, I am glad that you found the tool useful and helped to expand its usability! пн, 27 мая 2024 г. в 04:05, nikostr ***@***.***>:

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Hi! Thanks for this tool! I just wanted to let you know that I've created a PR to make DifCover installable through bioconda ( bioconda/bioconda-recipes#48098 <bioconda/bioconda-recipes#48098>). My reason for doing this is that it will make it easier to integrate DifCover scripts into snakemake pipelines and wrappers, but I hope it might be useful for others as well. — Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEGJB63G4J3KHVLJZ56VGPTZELSM3AVCNFSM6AAAAABIKWDUJSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMYTQNJRG4ZTEOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[nikostr]

My PR has now been merged into bioconda. To install DifCover into a new conda environment user with conda installed can simply type conda create -n difcover-env -c bioconda difcover, or simply do conda install -c bioconda difcover to install it into their currently active environment. Once the environment is active, all DifCover scripts can be run as they are. Run cp $(which run_difcover.sh) dest-dir to get a copy of run_difcover.sh to edit in your project directory. With the environment active the $FOLDER_PATH stuff can be omitted from the script.

[danielyao12]

Hi timnat and nikostr! I installed the DifCover through conda. When I run the command
from_unionbed_to_ratio_per_window_CC0 sample1_sample2.unionbedcv 10 219 10 240 1000 500,
it prompted that

Parameters:
a=1
A=1000000
b=1
B=1000000
v=1000
l=0

It seems that even though I set the a, A, b, B, and l as 10, 219, 10, 240, and 500, the function "from_unionbed_to_ratio_per_window_CC0" in the conda still read 1, 1000000, 1, 1000000, and 0. Is something wrong about the function "from_unionbed_to_ratio_per_window_CC0" in the conda?

Thank you very much for your time!

[timnat]

Hi Yao, I see a possible problem. The source code for DifCover was updated, but not the README file (I will work on it later). I am not sure which version was packaged in the conda. The syntax for input parameters was changed and now requires the name for each parameter. ./from_unionbed_to_ratio_per_window_CC0 Expected *.unionbed file Usage: [-a minimum depth of coverage for sample1 [0]] [-A maximum depth of coverage for sample1 [1000000]] [-b minimum depth of coverage for sample2 [0]] [-B maximum depth of coverage for sample2 [1000000]] [-v Target number of valid bases in the window [1000]] [-l minimum size of window to output [0]] sample1_sample2.unionbedcv I.e. for your example try to run from_unionbed_to_ratio_per_window_CC0 sample1_sample2.unionbedcv -a 10 -A 219 -b 10 -B 240 -v 1000 -l 500 Let me know if it helped to solve the problem, and I will update the description.

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On Tue, Dec 17, 2024 at 1:31 AM YAO Xin ***@***.***> wrote: Hi timnat and nikostr! I installed the DifCover through conda. When I run the command from_unionbed_to_ratio_per_window_CC0 sample1_sample2.unionbedcv 10 219 10 240 1000 500, it prompted that Parameters: a=1 A=1000000 b=1 B=1000000 v=1000 l=0 It seems that even though I set the a, A, b, B, and l as 10, 219, 10, 240, and 500, the function "from_unionbed_to_ratio_per_window_CC0" in the conda still read 1, 1000000, 1, 1000000, and 0. Is something wrong about the function "from_unionbed_to_ratio_per_window_CC0" in the conda? Thank you very much for your time! — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEGJB6YVTDBLZIRH5BOU2KL2F7AMJAVCNFSM6AAAAABTXWB7SKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBXGYYDOOJQGM> . You are receiving this because you commented.Message ID: ***@***.***>

[nikostr]

The version in conda is v3.0.1, the latest one published as a version here on github, so the solution proposed by you @timnat should solve the issue :)