Difference between bin/bs_call and gemBSbinaries/bs_call?

[dy-lin]

What is the difference between these two binaries?

/home/dlin/.conda/envs/gembs/bin/bs_call
/home/dlin/.conda/envs/gembs/lib/python3.9/site-packages/gemBS/gemBSbinaries/bs_call

I've noted that the first one does not have options such as -O and --contig-sizes.

The .vcf generated by bin/bs_call is also empty compared to that of gemBSbinaries/bs_call.

[dy-lin]

Looks like gemBS call use gemBSbnaries/bs_call instead of bin/bs_call... is there a reason for this?

[heathsc]

gemBS should use the binaries in gemBSbinaries. As for your original question about the difference between bin/bs_call and gemBSbinaries/bs_call, I think that that is a question for the maintainer of the conda package. Yours, Simon

…

On Fri, Dec 2, 2022 at 12:17 AM Diana Lin ***@***.***> wrote: Does gemBS call use gemBSbnaries/bs_call instead of bin/bs_call? — Reply to this email directly, view it on GitHub <#96 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAY465ZSAHKDIDS6ULO5LHLWLEWYRANCNFSM6AAAAAASQGRFAQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[dy-lin]

Hi Simon,

Thank you. I see that another package called bs_call is installed in the gemBS recipe:

  Updating specs:

   - gembs
   - ca-certificates
   - certifi
   - openssl


  Package                 Version  Build           Channel                    Size
────────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────────

  + bcftools               1.15.1  h0ea216a_0      bioconda/linux-64         884kB
  + brotli                  1.0.9  h166bdaf_8      conda-forge/linux-64       19kB
  + brotli-bin              1.0.9  h166bdaf_8      conda-forge/linux-64       20kB
  + bs_call                  2.02  h7c6eca5_6      bioconda/linux-64         231kB
  + contourpy               1.0.6  py39hf939315_0  conda-forge/linux-64      239kB
  + cycler                 0.11.0  pyhd8ed1ab_0    conda-forge/noarch       Cached
  + dill                    0.3.6  pyhd8ed1ab_1    conda-forge/noarch         83kB
  + fonttools              4.38.0  py39hb9d737c_1  conda-forge/linux-64        2MB
  + gem3-mapper             3.6.1  h67092d7_10     bioconda/linux-64         848kB
  + gembs              3.5.5_IHEC  py39ha087f92_5  bioconda/linux-64          17MB
  + htslib                 1.15.1  h6bc39ce_1      bioconda/linux-64           2MB
  + kiwisolver              1.4.4  py39hf939315_1  conda-forge/linux-64       78kB
  + libbrotlicommon         1.0.9  h166bdaf_8      conda-forge/linux-64       67kB
  + libbrotlidec            1.0.9  h166bdaf_8      conda-forge/linux-64       34kB
  + libbrotlienc            1.0.9  h166bdaf_8      conda-forge/linux-64      295kB
  + llvm-openmp             8.0.1  hc9558a2_0      conda-forge/linux-64      449kB
  + matplotlib-base         3.6.2  py39hf9fd14e_0  conda-forge/linux-64        8MB
  + multiprocess          0.70.14  py39hb9d737c_3  conda-forge/linux-64      220kB
  + munkres                 1.1.4  pyh9f0ad1d_0    conda-forge/noarch         12kB
  + mysql-connector-c      6.1.11  h6eb9d5d_1007   conda-forge/linux-64        3MB
  + openjpeg                2.5.0  h7d73246_1      conda-forge/linux-64      546kB
  + openmp                  8.0.1  0               conda-forge/linux-64        8kB
  + packaging                21.3  pyhd8ed1ab_0    conda-forge/noarch       Cached
  + pillow                  9.2.0  py39hf3a2cdf_3  conda-forge/linux-64       47MB
  + pyparsing               3.0.9  pyhd8ed1ab_0    conda-forge/noarch       Cached
  + samtools               1.15.1  h1170115_0      bioconda/linux-64         402kB
  + ucsc-bedtobigbed          377  ha8a8165_3      bioconda/linux-64         184kB
  + ucsc-wigtobigwig          377  ha8a8165_3      bioconda/linux-64         160kB
  + unicodedata2           15.0.0  py39hb9d737c_0  conda-forge/linux-64      512kB