Closed Rosmaninho closed 3 years ago
Are you certain that you have 0.12.6? You can check it with TOBIAS --version
.
For 0.12.6, with TOBIAS --help
, I get:
______________________________________________________________________________
| |
| ~ T O B I A S ~ |
| Transcription factor Occupancy prediction |
| By Investigation of ATAC-seq Signal |
|______________________________________________________________________________|
Usage: TOBIAS <TOOLNAME> [arguments]
Tools for footprinting analysis:
ATACorrect Correct reads with regards to Tn5 sequence bias
ScoreBigwig Calculate scores such as footprints from cutsites
BINDetect Detect TF binding from footprints and motifs
Tools for working with motifs/TFBS:
TFBScan Identify positions of TFBS given sequence and motifs
FormatMotifs Utility to deal with motif files
ClusterMotifs Cluster motifs by similarity
ScoreBed Score .bed-file with signal from .bigwig-file(s)
Visualization tools:
PlotAggregate Aggregate of .bigwig-signal across TF binding sites
PlotHeatmap Heatmap of .bigwig-signal across TF binding sites
PlotChanges Plot changes in TF binding across multiple conditions (from BINDetect output)
PlotTracks Plot genomic tracks using the svist4get package
Miscellaneous tools:
DownloadData Download test data for the TOBIAS tools
MergePDF Merge pdf files to one
MaxPos Get .bed-positions of highest bigwig signal within .bed-regions
SubsampleBam Subsample a .bam-file using samtools
CreateNetwork Create TF-gene network from annotated TFBS
Log2Table Convert logs from PlotAggregate to tab-delimitered tables of footprint stats
FilterFragments Tool for filtering fragments from a .bam-file based on the overlap of reads with .bed-regions
For help on each tool, please run: TOBIAS <TOOLNAME> --help
For version number: TOBIAS --version
Which contains ClusterMotifs.
I installed it following the instructions on https://github.com/loosolab/TOBIAS/wiki/installation with the TOBIAS_ENV. Apparently the TOBIAS version it installed is version 0.9.0.
Okay, I can't reproduce that on my end, but I made a small change in the tobias_env.yaml
, adjusting which might have caused the issue. I'm closing this since the solution was found.
Yeah I had the same issue when trying to install using the installation instructions. Conda downloads 0.9.0 instead of the current version
As title says... Sorry about all the issues opened...