###### tags: `TOOLS`
# Outils à tester

## Installés en "dev" par le user *"tools"*

/home/tools/work/.conda/envs/

/home/tools/save
└── TESTS
    ├── DATA
    │   └── OUTIL
    ├── EXPECTED
    │   └── OUTIL
    └── SCRIPTS
        └── OUTIL

| Tool | Release | Statut | Command line | Expected results | Tester | Comments |
|:---------------- |:----------------:|:----------------:|:----------------:|:----------------:|:----------------:|:------------------------------------------------------:|
| snakemake | 7.12.0 | 🚧 | | | | |
| vsearch | 2.21.1 | 🚧 | | | | |
| diamond | 2.0.15 | 🚧 | | | | |
| ppanggolin | 1.2.74 | 🚧 | | | | |
| genozip | 13.0.20 | 🚧 | | | | trop tard merci |
| nanoplot | 1.40.0 | 🚧 | | | | |
| antismash | 6.1.1 | 🚧 | | | | antismash --check-prereqs=>All prerequisites satisfied |
| trycycler | 0.5.3 | 🚧 | | | | |
| fastp | 0.23.2 | 🚧 | | | val | |
| busco | 5.4.3 | 🚧 | | | val | |
| SPAdes | 3.15.5 | 🚧 | | | val | |
| dREP | 3.4.0 | 🚧 | | | val | |
| --/////////////- | --/////////////- | --/////////////- | --/////////////- | --/////////////- | --/////////////- | --/////////////- |
| bowtie2 | new release :pushpin: | | | | | |
| kaiju | 1.9.2 | :+1: |/save_home/tools/TESTS/DATA/OUTIL/KAIJU/test.sh | /home/tools/save/TESTS/EXPECTED/OUTIL/KAIJU | vero | utilisation des scripts ok |
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> 🚧 A tester
> :angry: A revoir
> :+1: OK à cloner sur front
---

### Liste des outils d'intérêt déja mis à jour

| Tool | Release | Statut | Command line | Expected results | Tester | Comments |
|:--------- |:--------:|:------:|:-----------------------------------------------------:|:----------------------------------------------------------:|:-------:|:--------:|
| mmseqs2 | 14.7e284 | :+1: | save/TESTS/SCRIPTS/OUTIL/MMSEQS2/test.sh | save/TESTS/EXPECTED/OUTIL/MMSEQS2/alnRes.m8 | Vero | |
| bowtie2 | 2.4.5 | :+1: | bowtie2.sh | MycoplasmagenitaliumSampleVSMycoplasmagenitaliumL43967.sam | Val | |
| frogs | 4.0.1 | :+1: | `/save_home/tools/TESTS/DATA/OUTIL/FROGS/test.sh` | `/save_home/tools/TESTS/EXPECTED/OUTIL/FROGS` | Olivier | |
| frogsfunc | 4.0.1 | :+1: | `/save_home/tools/TESTS/DATA/OUTIL/FROGSFUNC/test.sh` | `/save_home/tools/TESTS/EXPECTED/OUTIL/FROGSFUNC` | Olivier | |
| kaiju | 1.9.0 | :+1: | `/save_home/tools/TESTS/DATA/OUTIL/KAIJU/test.sh` | `/home/tools/save/TESTS/EXPECTED/OUTIL/KAIJU` | Olivier | |
---

## Liste des outils qui peuvent être mis à jour

* ### (05/10/2022)

abyss-2.3.5
                ==> antismash-6.1.1  : fait
bakta-1.5.1
bamaddrg-9baba65f88228e55639689a3cea38dd150e6284f
bamtocov-2.7.0
bbmap-39.00
bcftools-1.16
beast-1.10.4
bedops-2.4.41
bibtexparser-1.4.0
bokeh-2.4.3
boto3-1.24.85
bowtie2-2.4.5
bracken-2.7
breseq-0.37.1
                = > busco-5.4.3  : fait
cafe-5.0.0
canu-2.2
checkm-genome-1.2.1
checkv-1.0.1
csvtk-0.25.0
cutadapt-4.1
dadi-2.2.0
delly-1.1.5
                ==> diamond-2.0.15  : fait
                ==> drep-3.4.0  : fait
ea-utils-1.1.2.779
eggnog-mapper-2.1.9
ena-webin-cli-5.0.0
entrez-direct-16.2
fastani-1.33
                ==> fastp-0.23.2  : fait
fastq-screen-0.15.2
fasttree-2.1.11
ffq-0.3.0
flye-2.9.1
freebayes-1.3.6
frogs-4.0.1
gatk4-4.2.6.1
gdal-3.5.2
genometools-1.2.1
genozip-14.0.9
get_homologues-3.5.4
graftm-0.14.0
gromacs-2022.3
gtdbtk-2.1.1
hdf5-1.12.2
hilinetojuicer-0.0.2
htseq-2.0.2
htslib-1.16
icescreen-1.0.4
instrain-1.6.3
interproscan-5.55_88.0
isescan-1.7.2.3
isonclust-0.0.6.1
jalview-2.11.2.4
jellyfish-2.2.10
julia-1.8.2
kaiju-1.9.0
kallisto-0.48.0
kraken-biom-1.2.0
krona-2.8.1
last-1411
lastz-1.04.15
macrel-1.2.0
macsyfinder-2.0
mafft-7.508
mamba-0.27.0
masurca-4.0.9
mauve-2.4.0.snapshot_2015_02_13
medaka-1.7.2
medusa-1.6
meme-5.4.1
metagenome-atlas-2.11.1
metaphlan-4.0.2
minia-3.2.6
minimap2-2.24
mirdeep2-2.0.1.3
mothur-1.48.0
msamtools-1.1.0
multiqc-1.13
muscle-5.1
nanoplot-1.40.2
ncbi-amrfinderplus-3.10.42
ncbi-datasets-cli-13.42.2
ncbi-genome-download-0.3.1
netpbm-10.73.41
nextflow-22.04.5
novoalign-4.03.04
ondamonitor-21.5.0
pandoc-2.19.2
parsnp-1.7.4
pastml-1.9.40
pftools-3.2.12
phanotate-1.5.0
pharokka-1.0.0
phylobayes-mpi-1.9
phylophlan-3.0.3
phyml-3.3.20211231
picard-2.27.4
picrust2-2.5.0
pilon-1.24
pipits-2.8
pipreqs-0.4.11
pirate-1.0.5
planemo-0.74.11
ppanggolin-1.2.74
prank-v.170427
primer3-2.6.1
prophet-1.1.1
pyani-0.2.12
pyseer-1.3.10
python2-secrets-1.0.5
qpdf-10.6.3
quast-5.2.0
racon-1.5.0
raven-assembler-1.8.1
raxml-ng-1.1.0
resfinder-4.1.11
rmblast-2.11.0
r-medicare-0.2.1
r-metalonda-1.1.8
r-meteor-0.3_4
r-pgirmess-2.0.0
r-reticulate-1.26
r-tabusearch-1.1.1
salmon-1.9.0
samtools-1.16.1
scikit-learn-1.1.2
seispy-1.2.18
selectsequencesfrommsa-1.0.5
seqkit-2.3.1
seqwish-0.7.6
shasta-0.8.0
showit-1.1.4
snakemake-7.15.1
sniffles-2.0.7
sortmerna-4.3.6
sourmash-4.5.0
spacepharer-5.c2e680a
                    ==> spades-3.15.5 : fait
sra-tools-3.0.0
stacks-2.61
star-2.7.10a
staramr-0.8.0
stringtie-2.2.1
super-focus-1.6
taxonkit-0.13.0
toulligqc-2.2.2
trinity-2.13.2
trycycler-0.5.3
ucsc-bedgeneparts-377
validate-fasta-database-1.0
vcflib-1.0.3
vcontact2-0.11.3
viennarna-2.5.1
vsearch-2.21.2
wham-1.8.0.1.2017.05.03
xontrib-argcomplete-0.3.1
xorg-xproxymanagementprotocol-1.0.3
zdesk-2.8.1
zpaq-7.15

### Pb avec :

- novoalign 4.03.04 :exclamation::exclamation:

========================= Novoalign information ===========================================
Novoalign is installed. Documentation installed in
/home/tools/work/.conda/envs/novoalign-4.03.04/share/doc/novoalign

Commercial use requires a license; contact [e-mail].
License also adds multi-threading and other features.
Once you have a license file, run novoalign-license-register to install it.

Licensing information from Novocraft website:
--------------------------------------------------------------------------------------------
Novoalign with some limitations is free for use by non-profit organisations.
Commercial users should contact [e-mail] to purchase a license.
A license enables
* Multi-threading
* Gzipped input files
* Amplicon mode
and much more.
You must include a copy of this license if you share any Novocraft programs.
======================== End of novoalign information ======================================


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