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update taxids list
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@bodeolukolu
bodeolukolu committed Apr 9, 2024
1 parent 88edb8e commit 8856b2f
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58 changes: 29 additions & 29 deletions Qmatey
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Expand Up @@ -68,36 +68,36 @@ if [[ -d "$Qmatey_dir/tools" ]] && [[ -z $(ls -A "$Qmatey_dir/tools") ]] ; then
fi

cd $Qmatey_dir/tools
if [ ! -d bwa* ]; then echo -e "${magenta}- BWA is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d samtools* ]; then echo -e "${magenta}- samtools is not installated or properly installed\n- Consider checking dependencies and re-running install command ${white}"; fi
if [ ! -d bwa* ]; then echo -e "${magenta}- BWA is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d samtools* ]; then echo -e "${magenta}- samtools is not installed or is not properly installed\n- Consider checking dependencies and re-running install command ${white}"; fi
if [ ! -d samtools* ]; then echo -e "${magenta}- else, GBSapp will attempt using the system-installed verion of samtools\n\n ${white}"; fi
if [ ! -f picard* ]; then echo -e "${magenta}- PICARD is not installated or properly installed\n- Consider re-running install command\n\n ${white}"; fi
if [ ! -d jdk* ]; then echo -e "${magenta}- Java jdk8 is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d cd-hit* ]; then echo -e "${magenta}- cd-hit is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ncbi-blast* ]; then echo -e "${magenta}- NCBI-BLAST is not installated or properly installed\n- Consider re-running install command\n\n ${white}"; fi
if [ ! -d ./R/plotly* ]; then echo -e "${magenta}- R-package plotly is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/plotly ]; then echo -e "${magenta}- R-package plotly is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/htmlwidgets ]; then echo -e "${magenta}- R-package htmlwidgets is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/data.table ]; then echo -e "${magenta}- R-package data.table is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/plyr ]; then echo -e "${magenta}- R-package plyr is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/dplyr ]; then echo -e "${magenta}- R-package dplyr is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/rlang ]; then echo -e "${magenta}- R-package rlang is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/generics ]; then echo -e "${magenta}- R-package generics is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/tidyselect ]; then echo -e "${magenta}- R-package tidyselect is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/Rcpp ]; then echo -e "${magenta}- R-package Rcpp is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/reshape2 ]; then echo -e "${magenta}- R-package reshape2 is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/ggplot2 ]; then echo -e "${magenta}- R-package ggplot2 is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/fansi ]; then echo -e "${magenta}- R-package fansi is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/ggcorrplot ]; then echo -e "${magenta}- R-package ggcorrplot is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/stringi ]; then echo -e "${magenta}- R-package stringi is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/stringr ]; then echo -e "${magenta}- R-package stringr is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/magrittr ]; then echo -e "${magenta}- R-package magrittr is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/infotheo ]; then echo -e "${magenta}- R-package infotheo is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/gtools ]; then echo -e "${magenta}- R-package gtools is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/gtable ]; then echo -e "${magenta}- R-package gtable is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/assertthat ]; then echo -e "${magenta}- R-package assertthat is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/plotme ]; then echo -e "${magenta}- R-package plotme is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/CCLasso ]; then echo -e "${magenta}- R-package is not installated or properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -f picard* ]; then echo -e "${magenta}- PICARD is not installed or is not properly installed\n- Consider re-running install command\n\n ${white}"; fi
if [ ! -d jdk* ]; then echo -e "${magenta}- Java jdk8 is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d cd-hit* ]; then echo -e "${magenta}- cd-hit is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ncbi-blast* ]; then echo -e "${magenta}- NCBI-BLAST is not installed or is not properly installed\n- Consider re-running install command\n\n ${white}"; fi
if [ ! -d ./R/plotlyGeoAssets ]; then echo -e "${magenta}- R-package plotly is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/plotly ]; then echo -e "${magenta}- R-package plotly is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/htmlwidgets ]; then echo -e "${magenta}- R-package htmlwidgets is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/data.table ]; then echo -e "${magenta}- R-package data.table is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/plyr ]; then echo -e "${magenta}- R-package plyr is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/dplyr ]; then echo -e "${magenta}- R-package dplyr is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/rlang ]; then echo -e "${magenta}- R-package rlang is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/generics ]; then echo -e "${magenta}- R-package generics is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/tidyselect ]; then echo -e "${magenta}- R-package tidyselect is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/Rcpp ]; then echo -e "${magenta}- R-package Rcpp is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/reshape2 ]; then echo -e "${magenta}- R-package reshape2 is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/ggplot2 ]; then echo -e "${magenta}- R-package ggplot2 is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/fansi ]; then echo -e "${magenta}- R-package fansi is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/ggcorrplot ]; then echo -e "${magenta}- R-package ggcorrplot is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/stringi ]; then echo -e "${magenta}- R-package stringi is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/stringr ]; then echo -e "${magenta}- R-package stringr is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/magrittr ]; then echo -e "${magenta}- R-package magrittr is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/infotheo ]; then echo -e "${magenta}- R-package infotheo is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/gtools ]; then echo -e "${magenta}- R-package gtools is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/gtable ]; then echo -e "${magenta}- R-package gtable is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/assertthat ]; then echo -e "${magenta}- R-package assertthat is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/plotme ]; then echo -e "${magenta}- R-package plotme is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi
if [ ! -d ./R/CCLasso ]; then echo -e "${magenta}- R-package is not installed or is not properly installed\n- Consider checking dependencies and re-running install command\n\n ${white}"; fi



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9 changes: 8 additions & 1 deletion README.md
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Expand Up @@ -315,7 +315,9 @@ annotate_seq=false


## Select Article Referencing Qmatey
1. manuscript in preparation
1. Adams AK, Kristy BD, Gorman M, Balint-Kurti P, Yencho GC, and Olukolu BA. (2023) Qmatey: An automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes. Briefings in Bioinformatics. 24 (6): bbad351.

2. Adams A, Landry D., Sykes V, Rickman T, Cham A, Timling A, Kelly H, McBeath JH, and Olukolu BA (2024) Maize Kernel-Associated Metagenomes Reveal Potential Microbe-Microbe Interactions that Underlie Fusarium Ear Rot Disease. Phytobiomes. doi.org/10.1094/PBIOMES-07-23-0074-R


## Troubleshooting
Expand Down Expand Up @@ -350,6 +352,11 @@ While the installation of samtools are automated, the installation requires some
- Re-submit job with appropriate values or modify header of the Qmatey_run.sh batch file.
- If using compute cluster managers other than SLURM, header of Qmatey_run.sh batch can also be modified to fit the syntax of the cluster manager been used.
```
**Problem with amount of memory and/or processors/cores specified:**<br />
```
- If BLAST search fails after updating NCBI database, consider updating the list of taxids in the taxids directory.
- You can use script in the Generate_taxids.sh file to update the taxid list.
```
## Versioning
Versioning will follow major.minor.patch <a href="https://semver.org">semantic versioning format</a>.
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