Update Busco to 5.2.2 and container entrypoint fix.

[mahesh-panchal]

Update Busco to 5.2.2 Fixes error arising from changed container entrypoint

.command.sh: line 2: AUGUSTUS_CONFIG_PATH: unbound variable

Include mamba profiles

Closes #68

Notes: Conda seems to run out of memory creating environment Error code 143 Mamba has some other error, Error code 120.

[LucileSol]

If I do

nextflow run -c params.config -profile nbis,singularity /git/NBIS/mahesh/pipelines-nextflow/AnnotationPreprocessing/AnnotationPreprocessing.nf 

Error executing process > 'annotation_preprocessing:busco (genome_uppercase_purified.fa)'                                       
Caused by:
  Process `annotation_preprocessing:busco (genome_uppercase_purified.fa)` terminated with an error exit status (1)

Command executed:

  if [ ! -w "${AUGUSTUS_CONFIG_PATH}" ]; then
executor >  slurm (6)
[6b/6feaae] process > annotation_preprocessing:assembly_purify (genome_uppercase ; min length = ... [100%] 1 of 1 ✔
[b9/0deed9] process > annotation_preprocessing:assembly_generate_stats (genome_uppercase_purified)  [100%] 2 of 2 ✔
[95/2d5482] process > annotation_preprocessing:busco (genome_uppercase_purified.fa)                 [150%] 3 of 2, failed: 3 ✘
Error executing process > 'annotation_preprocessing:busco (genome_uppercase_purified.fa)'

Caused by:
  Process `annotation_preprocessing:busco (genome_uppercase_purified.fa)` terminated with an error exit status (1)

Command executed:

  if [ ! -w "${AUGUSTUS_CONFIG_PATH}" ]; then
      # Create writable tmp directory for augustus
      AUG_CONF_DIR=$( mktemp -d -p $PWD )
      cp -r $AUGUSTUS_CONFIG_PATH/* $AUG_CONF_DIR
      export AUGUSTUS_CONFIG_PATH=$AUG_CONF_DIR
  fi
  # before with buscov4 it was echo "BUSCO_CONFIG_FILE=$BUSCO_CONFIG_FILE", it stops working for buscov5
  echo "BUSCO_CONFIG_FILE=$AUGUSTUS_CONFIG_PATH/myconfig.ini"
  echo "AUGUSTUS_CONFIG_PATH=$AUGUSTUS_CONFIG_PATH"                                                                              busco -c 8 -i genome_uppercase_purified.fa -l bacteria_odb10 -m genome --out busco_genome_uppercase_purified_bacteria_odb10

Command exit status:
  1

Command output:
  BUSCO_CONFIG_FILE=/scratch/nxf.rGAYkN1Ist/tmp.Ttyd5yHyME/myconfig.ini
  AUGUSTUS_CONFIG_PATH=/scratch/nxf.rGAYkN1Ist/tmp.Ttyd5yHyME
  this version of pandas is incompatible with numpy < 1.16.5
  your numpy version is 1.16.4.                                                                                                  Please upgrade numpy to >= 1.16.5 to use this pandas version
  There was a problem installing BUSCO or importing one of its dependencies. See the user guide and the GitLab issue board (https://gitlab.com/ezlab/busco/issues) if you need further assistance.

Command wrapper:
  nxf-scratch-dir node-a01:/scratch/nxf.rGAYkN1Ist
  BUSCO_CONFIG_FILE=/scratch/nxf.rGAYkN1Ist/tmp.Ttyd5yHyME/myconfig.ini
  AUGUSTUS_CONFIG_PATH=/scratch/nxf.rGAYkN1Ist/tmp.Ttyd5yHyME
  this version of pandas is incompatible with numpy < 1.16.5
  your numpy version is 1.16.4.
  Please upgrade numpy to >= 1.16.5 to use this pandas version
  There was a problem installing BUSCO or importing one of its dependencies. See the user guide and the GitLab issue board (https://gitlab.com/ezlab/busco/issues) if you need further assistance.

Work dir:
  /projects/annotation/Lepidium_7/pacbio/hybrid_campestre_heterophyllum_LcxLh/genome/work/06/6aac4928781255d5d565e2767f092c

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

[mahesh-panchal]

Running the docker container is showing a different numpy version.

$ docker run -it --rm quay.io/biocontainers/busco:5.2.2--pyhdfd78af_0 bash
root@75dc09e22c1d:/# python
Python 3.9.6 | packaged by conda-forge | (default, Jul 11 2021, 03:39:48) 
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> print(numpy.__version__)
1.21.1
>>> 

This either means I'm not using the correct python inside the container, or some python libs from outside the singularity container are being loaded perhaps via hidden folders in $HOME.

[LucileSol]

all working now