Software
========

| giptools provides the following software installed in ubuntu xenial.
| Ubuntu xenial is covered by the Creative Commons CC-BY-SA version 3.0 UK `licence <https://ubuntu.com/legal/intellectual-property-policy>`_
| Links to download the software source code are provided and accessible to general public. 
| Source code of third party software is available from giptools at the container location /opt/source_code
| The license and copyright notice of the tools are also available from giptools at the container location /opt/licenses.tar.gz

| **samtools**
| Version 1.8 
| :download:`License & Copyright <LICENSE_samtools>`
| `Source code <https://github.com/samtools/samtools/archive/1.8.tar.gz>`_

| **freebayes**        
| Version 1.3.2
| :download:`License & Copyright <LICENSE_freebayes>`
| `Source code <https://github.com/ekg/freebayes/archive/v1.3.2.tar.gz>`_

| **bwa**              
| Version 0.7.17
| :download:`License & Copyright <COPYING_bwa>`
| `Source code <https://github.com/lh3/bwa/archive/v0.7.17.tar.gz>`_

| **htslib**         
| Version 1.8        
| :download:`License <LICENSE_htslib>`
| `Source code <https://github.com/samtools/htslib/archive/1.8.tar.gz>`_

| **bedtools**      
| Version 2.29.2     
| :download:`License <LICENSE_bedtools>`
| `Source code <https://github.com/arq5x/bedtools2/archive/v2.29.2.tar.gz>`_

| **Python3**       
| Version 3.7.0      
| :download:`License <LICENSE_Python3>`
| `Source code <https://www.python.org/ftp/python/3.7.0/Python-3.7.0.tgz>`_

| **bcftools**         
| Version 1.11      
| :download:`License <LICENSE_bcftools>`
| `Source code <https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2>`_         

| **deeptools**        
| Version 3.5.1      
| :download:`License <LICENSE_deepTools>`
| `Source code <https://github.com/deeptools/deepTools/archive/refs/tags/3.5.1.tar.gz>`_       

| **RepeatMasker**     
| Version 4.1.0      
| :download:`License <LICENSE_RepeatMasker>` 
| `Source code <http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.0.tar.gz>`_

| **rmblast**          
| Version 2.10.0+    
| :download:`License <LICENSE_rmblast>`           
| `Source code <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz>`_

| **trf**              
| Version 4.09.1     
| :download:`Copyright <COPYING_trf>`                   
| `Source code <https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1.tar.gz>`_

| **mummer**           
| Version 4.0.0rc1   
| :download:`License <LICENSE_mummer>`   
| :download:`Copyright <COPYRIGHT_mummer>`
| `Source code <https://github.com/mummer4/mummer/archive/v4.0.0rc1.tar.gz>`_          

| **snpEff**           
| Version 4.3t       
| `License <https://pcingola.github.io/SnpEff/license/>`_  
| `Source code <https://github.com/pcingola/SnpEff/archive/v4.3t.tar.gz>`_

| **cdhit**            
| Version 4.8.1      
| :download:`License & copyright <LICENSE_cdhit>`   
| `Source code <https://github.com/weizhongli/cdhit/archive/V4.8.1.tar.gz>`_            

| **R**                
| Version 3.6.0      
| :download:`License & copyright <COPYING_R>`                        
| `Source code <https://cran.r-project.org/src/base/R-3/R-3.6.0.tar.gz>`_

| **circos**           
| Version 0.69-9     
| :download:`License & copyright <LICENSE_circos>`             
| `Source code <http://circos.ca/distribution/circos-0.69-9.tgz>`_

| **picard**           
| Version 2.18.9     
| :download:`License & copyright <LICENSE_picard>`             
| `Source code <https://github.com/broadinstitute/picard/archive/2.18.9.tar.gz>`_

| **delly**            
| Version 0.8.7      
| :download:`License & copyright <LICENSE_delly>`  
| `Source code <https://github.com/dellytools/delly/archive/v0.8.7.tar.gz>`_             

| **bedGraphToBigWig** 
| Version 2.8        
| `License <https://genome.ucsc.edu/license/>`_                            

| **Red**              
| Version 05/22/2015 
| `License <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0654-5>`_
| `Source code <http://toolsmith.ens.utulsa.edu/red/data/DataSet1Src.tar.gz>`_

| **IQ-tree2**         
| Version 2.1.2      
| `GNU-GPL License <http://www.iqtree.org/about/>`_       


Additionally giptools includes the following R packages:
ape,
argparse,
Biostrings,
bisoreg,
data.table,
dplyr,
entropy,
FactoMineR,
fastcluster,
fields,
fitdistrplus,
GenomicRanges,
ggExtra,
ggplot2,
ggridges,
ggtern,
ggtree,
gplots,
gridExtra,
gtools,
igraph,
IRanges,
karyoploteR,
knitr,
MASS,
MCL,
mclust,
mixtools,
networkD3,
openxlsx,
pheatmap,
plot3D,
png,
RColorBrewer,
reshape2,
scales,
seqLogo,
session,
VariantAnnotation,
venn,

These packages and their dependencies are available at the container location: /usr/local/lib/R/library/