Empty output for odgi version command

[heuermh]

The version string for the 0.6.2 release version available on Bioconda is missing from the odgi help and odgi version commands.

$ docker run -it quay.io/biocontainers/odgi:0.6.2--py39h98c8e45_0 /bin/bash                      
root@66101d6c6e4d:/# odgi                                                                                                                             
odgi: optimized dynamic genome/graph implementation, version                                                                                          

usage: odgi <command> [options]                                                                                                                       

Overview of available commands:                                                                                                                       
  -- bin           Binning of pangenome sequence and path information in the graph.                                                                   
  -- break         Break cycles in the graph and drop its paths.                                                                                      
  -- build         Construct a dynamic succinct variation graph in ODGI format from a GFAv1.                                                          
  -- chop          Divide nodes into smaller pieces preserving node topology and order.                                                               
  -- cover         Cover the graph with paths.                                                                                                        
  -- crush         Crush runs of N.                                                                                                                   
  -- degree        Describe the graph in terms of node degree.                                                                                        
  -- depth         Find the depth of a graph as defined by query criteria. Without specifying any non-mandatory options, it prints in a tab-delimited format path, start, end, and mean.depth to stdout.                                                                                                    
  -- draw          Draw previously-determined 2D layouts of the graph with diverse annotations.                                                       
  -- explode       Breaks a graph into connected components storing each component in its own file.                                                   
  -- extract       Extract subgraphs or parts of a graph defined by query criteria.                                                                   
  -- flatten       Generate linearizations of a graph.                                                                                                
  -- groom         Resolve spurious inverting links.                                                                                                  
  -- kmers         Display and characterize the kmer space of a graph.                                                                                
  -- layout        Establish 2D layouts of the graph using path-guided stochastic gradient descent (the graph must be sorted and id-compacted).       
  -- matrix        Write the graph topology in sparse matrix formats.                                                                                 
  -- normalize     Compact unitigs and simplify redundant furcations.                                                                                 
  -- overlap       Find the paths touched by given input paths.                                                                                       
  -- panpos        Get the pangenome position of a given path and nucleotide position (1-based).                                                      
  -- pathindex     Create a path index for a given graph.                                                                                             
  -- paths         Interrogate the embedded paths of a graph. Does not print anything to stdout by default!                                           
  -- position      Find, translate, and liftover graph and path positions between graphs. Results are printed to stdout.                              
  -- prune         Remove complex parts of the graph.                                                                                                 
  -- server        Start a basic HTTP server with a given path index file to go from *path:position* to *pangenome:position* very efficiently.        
  -- sort          Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm.                     
  -- squeeze       Squeezes multiple graphs in ODGI format into the same file in ODGI format.                                                         
  -- stats         Metrics describing a variation graph and its path relationship.                                                                    
  -- tips          Identifying break point positions relative to given query (reference) path(s) of all the tips in the graph or of tips of given path(s). Prints BED records to stdout.                                                                                                                    
  -- unchop        Merge unitigs into a single node preserving the node order.                                                                        
  -- unitig        Output unitigs of the graph.                                                                                                       
  -- untangle      Project paths into reference-relative (optionally PAF), to decompose paralogy relationships.                                       
  -- validate      Validate a graph checking if the paths are consistent with the graph topology.                                                     
  -- version       Print the version of ODGI to stdout.                                                                                               
  -- view          Project a graph into other formats.                                                                                                
  -- viz           Visualize a variation graph in 1D.                                                                                                 

root@66101d6c6e4d:/# odgi version                                                                                                                     

This is required for https://github.com/nf-core/pangenome/issues/70 and https://github.com/nf-core/modules/issues/1136 and several other related odgi new module issues.

[AndreaGuarracino]

That is strange. Unfortunately, we have problems in updating the bioconda recipe due to a recent 1-hour limitation on the CircleCI build (https://github.com/bioconda/bioconda-recipes/pull/31655). Hope to fix that soon (I also caught a problem related to this versioning. Will fix that too).

[AndreaGuarracino]

I confirm that there was a problem regarding the versioning in the release process, which I have just fixed. There remains the CircleCI limit to defeat.

[heuermh]

Cool, thanks for the update!

[subwaystation]

ODGI v0.6.3 is now on Bioconda. This should be fixed @heuermh!