Updating Changelog, README and TODO

parent f5cb836a
Done v0.5.2:
-Fixed various issues with the building process and the precompiled binary:
-The precompiled binary was not portable enough. Now we added a script to create a portable binary inspired by https://pmelsted.wordpress.com/2015/10/14/building-binaries-for-bioinformatics/.
-The script can be found in folder portable_binary_builder
-Fixed some bugs with CMAKE_ARGS in boostSuperBuild/SuperBuild.cmake
-Added five new parameters to deal with binary incompatibility of the executables that are bundled with DBGWAS (GEMMA, Blast suite, phantomjs):
<TODO>: put the 5 parameters
-The precompiled binary was not portable enough. Now we added a script to create a portable binary inspired by https://pmelsted.wordpress.com/2015/10/14/building-binaries-for-bioinformatics/;
-The script can be found in folder portable_binary_builder;
-The new precompiled binary (v0.5.2) is portable now;
-Fixed some bugs with CMAKE_ARGS in boostSuperBuild/SuperBuild.cmake;
-Updated GEMMA to a portable static binary;
-This binary is build using Holy Build Box in https://github.com/leoisl/gemma0.93b
-Changed parameters -nc_db and -pt_db to -nc-db and -pt-db , in order to keep consistency with the other parameters naming
-Added five new parameters to deal with binary incompatibility of the executables that are bundled with DBGWAS (GEMMA, Blast suite, phantomjs):
-GEMMA-path , -Blast-path , -phantomjs-path , -no-preview , and -Rscript-path
-Replaced std::regex to boost::regex;
-Added an automated test based on the 282 pseudomonas_aeruginosa dataset;
-Improved well README.md;
......
......@@ -62,7 +62,7 @@ For reproducibility reasons, in the following you have easily the input data, an
3. UniProt database: https://www.dropbox.com/s/9y1p0yw918ips6k/uniprot_sprot_bacteria_for_DBGWAS.fasta?dl=1
4. Extract everything in the `bin` of the [precompiled binary](#downloading-the-precompiled-binaries) folder and execute DBGWAS as:
```
./DBGWAS -strains pseudomonas_aeruginosa_full_dataset/strains -newick pseudomonas_aeruginosa_full_dataset/strains.newick -nc_db Resistance_DB_for_DBGWAS.fasta -pt_db uniprot_sprot_bacteria_for_DBGWAS.fasta
./DBGWAS -strains pseudomonas_aeruginosa_full_dataset/strains -newick pseudomonas_aeruginosa_full_dataset/strains.newick -nc-db Resistance_DB_for_DBGWAS.fasta -pt-db uniprot_sprot_bacteria_for_DBGWAS.fasta
```
5. After finishing the execution, the output can be found in the folder ```bin/output/visualisations```
......@@ -174,8 +174,8 @@ You can find DBGWAS parameters by running ```./DBGWAS -h``` or simply here:
-strains (1 arg) : A text file describing the strains containing 3 columns: 1) ID of the strain; 2) Phenotype (0/1/NA); 3) Path to a multi-fasta file containing the sequences of the strain. This file needs a header. Check the sample_example folder or https://gitlab.com/leoisl/dbgwas/raw/master/sample_example/strains for an example.
-k (1 arg) : K-mer size. [default '31']
-newick (1 arg) : Optional path to a newick tree file. If (and only if) a newick tree file is provided, the lineage effect analysis is computed and PCs figures are generated. [default '']
-nc-db (1 arg) : A list of Fasta files separated by comma containing annotations in a nucleotide alphabet format (e.g.: -nc_db path/to/file_1.fa,path/to/file_2.fa,etc). You can customize these files to work better with DBGWAS (see https://gitlab.com/leoisl/dbgwas/tree/master#customizing-annotation-databases). [default '']
-pt-db (1 arg) : A list of Fasta files separated by comma containing annotations in a protein alphabet format (e.g.: -pt_db path/to/file_1.fa,path/to/file_2.fa,etc). You can customize these files to work better with DBGWAS (see https://gitlab.com/leoisl/dbgwas/tree/master#customizing-annotation-databases). [default '']
-nc-db (1 arg) : A list of Fasta files separated by comma containing annotations in a nucleotide alphabet format (e.g.: -nc-db path/to/file_1.fa,path/to/file_2.fa,etc). You can customize these files to work better with DBGWAS (see https://gitlab.com/leoisl/dbgwas/tree/master#customizing-annotation-databases). [default '']
-pt-db (1 arg) : A list of Fasta files separated by comma containing annotations in a protein alphabet format (e.g.: -pt-db path/to/file_1.fa,path/to/file_2.fa,etc). You can customize these files to work better with DBGWAS (see https://gitlab.com/leoisl/dbgwas/tree/master#customizing-annotation-databases). [default '']
-output (1 arg) : Path to the folder where the final and temporary files will be stored. [default 'output']
-skip1 (0 arg) : Skips Step 1, running only Steps 2 and 3. Assumes that Step 1 was correctly run and folder "step1" is present in the output folder.
-skip2 (0 arg) : Skips Steps 1 and 2, running only Step 3. Assumes that Steps 1 and 2 were correctly run and folders "step1" and "step2" are present in the output folder.
......
......@@ -2,10 +2,7 @@
TODO list
---------------------------------------------------------------------------------------------------------------------------------------------
Paper:
-Test on old ubuntu, debian, centOs, etc
-Put S1 online, and increment it to be a user-manual
- nc_db e pt_db para nc-db e pt-db
-Test on ubuntu, debian, openSuse, and any other OS we can;
-Table to track the performance of DBGWAS
-Subsampling SA, PA and TB big datasets
-100, 250, 500, 1000, 2500, 5000 10000
......@@ -18,7 +15,9 @@ Paper:
-Parse output file and create the following table:
Species Nb_Genome RunNb Time Mem
-Magali generate the graph
-Changed all mentions of -nc_db and -pt_db to -nc-db and -pt-db in the text;
-Put S1 online, and increment it to be a user-manual
-Other stuff needed for the paper (prioritize code, then test, then text)...
Next release (v0.5.2 ETA 31/05/2018):
......@@ -41,8 +40,6 @@ Priority:
3) Do a text output of DBGWAS so users can use other tools to post-process its output
4) Make step 3 multithreaded
5) Add to DBGWAS parameter -runOnlyStep1 Freq/Bin
-It will just produces the variant matrices and stop
-Freq = use frequences
......
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