Comments (3)
Looks like gemBS call
use gemBSbnaries/bs_call
instead of bin/bs_call
... is there a reason for this?
from gembs.
from gembs.
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
from gembs.
Related Issues (20)
- mapped bam files: SM key without value
- Logging error on call HOT 2
- how to set the control sequences?
- PBAT dataset failed in calling step HOT 3
- Can't see colors for ENCODE bigBed on UCSC browser HOT 4
- Scattering gemBS alignment step across a cluster HOT 1
- Conversion rate is N/A in QC HOT 7
- Latest version to Bioconda? HOT 9
- Dealing with overlapping reads HOT 3
- gemBS 3.5.1 issue at map stage of sample data HOT 10
- ValueError: Error while executing the Bisulfite bisulphite-mapping HOT 14
- Alignment Modes HOT 9
- Error when running gemBS map HOT 3
- HowTo enable GPU for read mapping? HOT 7
- mapping merge fails if one of the file_id's is equal to the Barcode
- The .bed file does not match the statistics of the REPORT
- System.Error::Signal raised (no=11) using bs_call HOT 2
- snp extract "Invalid format" HOT 4
- bs_call finished with -6
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from gembs.