Merge pull request #46 from molbiodiv/develop

Version 1.2.0

.github/workflows/test_perl.yml

@@ -0,0 +1,15 @@
+name: PerlTest
+on: [push]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: shogo82148/actions-setup-perl@v1
+      with:
+        perl-version: '5.34'
+    - run: sudo apt-get install -y muscle hmmer raxml prodigal
+    - run: curl http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z | tar xz
+    - run: echo "$PWD/Gblocks_0.91b" >> $GITHUB_PATH
+    - run: cpanm --installdeps .
+    - run: prove -lv t

CITATION.cff

@@ -0,0 +1,38 @@
+cff-version: 1.2.0
+message: If you use this software, please cite both the software and the paper (see preferred-citation).
+authors:
+  - family-names: Ankenbrand
+    given-names: "Markus J"
+    orcid: 0000-0002-6620-807X
+    affiliation: "Center for Computational and Theoretical Biology, University of Würzburg, Germany"
+    email: [email protected]
+  - family-names: Keller
+    given-names: Alexander
+    orcid: 0000-0001-5716-3634
+    affiliation: "Center for Computational and Theoretical Biology, University of Würzburg, Germany"
+title: bcgTree
+version: 1.2.0
+doi: 10.5281/zenodo.597913
+date-released: 2021-10-27
+repository-code: https://github.com/molbiodiv/bcgTree
+keywords:
+  - Phylogeny
+  - Alignment
+  - Evolution
+license: MIT
+url: https://github.com/molbiodiv/bcgTree
+preferred-citation:
+  type: article
+  scope: Cite this paper if you used bcgTree in your research
+  authors:
+    - family-names: Ankenbrand
+      given-names: Markus J
+    - family-names: Keller
+      given-names: Alexander
+  title: "bcgTree: automatized phylogenetic tree building from bacterial core genomes"
+  year: 2016
+  journal: Genome
+  volume: 59
+  issue: 10
+  doi: 10.1139/gen-2015-0175
+  url: https://doi.org/10.1139/gen-2015-0175

README.org

@@ -32,13 +32,14 @@ The following extra frameworks are used (included):
  - [[https://swingx.java.net/][SwingX]] 1.6.5 ([[http://www.gnu.org/copyleft/lesser.html][LGPL]])
 *** External programs
 bcgTree is a wrapper around multiple existing tools.
-The following external programs are called by bcgTree and have to be installed.
+The following external programs are called by bcgTree and have to be installed (~prodigal~ is optional, it is only needed if you provide nucleotide sequences using ~--genome~).
 The specified versions are the ones we used for testing (older versions might or might not work).
 Newer versions should work (otherwise feel free to open an issue).
- - [[http://hmmer.org/][hmmsearch]] (HMMER version 3.1b1) - Eddy et al, 2010. HMMER3: a new generation of sequence homology search software.
- - [[http://www.drive5.com/muscle/][muscle]] (v3.8.31) - Edgar et al, 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797.
+ - [[http://hmmer.org/][hmmsearch]] (HMMER version 3.3) - Eddy et al, 2010. HMMER3: a new generation of sequence homology search software.
+ - [[http://www.drive5.com/muscle/][muscle]] (v3.8.1551) - Edgar et al, 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797.
  - [[http://molevol.cmima.csic.es/castresana/Gblocks.html][Gblocks]] (version 0.91b) - Castresana et al, 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552.
- - [[http://sco.h-its.org/exelixis/web/software/raxml/][RAxML]] (version 8.2.4) - Stamatakis et al, 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313.
+ - [[http://sco.h-its.org/exelixis/web/software/raxml/][RAxML]] (version 8.2.12) - Stamatakis et al, 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313.
+ - [[https://github.com/hyattpd/Prodigal][prodigal]] (version 2.6.3) - Hyatt et al, 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119
 Additionally [[https://github.com/BioInf-Wuerzburg/SeqFilter][SeqFilter]] (Hackl et al, 2014. proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics 30, 3004-3011) is needed but it is included in this repo.
 *** Data
 There are two hmm files included in the data directory.
@@ -64,7 +65,7 @@ java -jar bcgTree.jar
 The graphical user interface is just a convenient way to call bcgTree.
 Usage is meant to be self-explanatory, any suggestions for improvement are welcome (please open an [[https://github.com/molbiodiv/bcgTree/issues][issue]]).
 In fact it adds no extra functionality it just collects the parameters and calls the perl script on the command line.
-The output is written to a text field as well as a log file.
+The output is written to a text field as well as a log file (bcgTree.log in the output folder).
 In order to preserve replicability all parameters are written in a file called options.txt in the output folder.
 The internal call of bcgTree is then just:
 #+BEGIN_SRC sh
@@ -78,8 +79,6 @@ Nevertheless here are some screenshots of the GUI:
 [[doc/screenshot1.png]]
 #+ATTR_HTML: :width 640
 [[doc/screenshot2.png]]
-#+ATTR_HTML: :width 640
-[[doc/screenshot3.png]]
 *** Command line
 #+BEGIN_SRC sh
 Usage:
@@ -95,7 +94,15 @@ Options:
 
     --proteome <ORGANISM>=<FASTA> [--proteome <ORGANISM>=<FASTA> ..]
                              Multiple pairs of organism and proteomes as
-                             fasta file paths
+                             peptide fasta file paths Attention: If you
+                             provide a proteome and genome with the same
+                             name, only the genome will be used.
+
+    --genome <ORGANISM>=<FASTA> [--genome <ORGANISM>=<FASTA> ..]
+                             Multiple pairs of organism and genomes as
+                             nucleotide fasta file paths. Attention: If you
+                             provide a proteome and genome with the same
+                             name, only the genome will be used.
 
     [--outdir <STRING>]      output directory for the generated output files
                              (default: bcgTree)
@@ -126,6 +133,10 @@ Options:
     [--raxml-bin=<FILE>]     Path to the raxml binary file. Default tries if
                              raxmlHPC is in PATH;
 
+    [--prodigal-bin=<FILE>]
+        Path to the prodigal binary file. Default tries if prodigal is in
+        PATH;
+
     [--threads=<INT>]
         Number of threads to be used (currently only relevant for raxml).
         Default: 2 From the raxml man page: PTHREADS VERSION ONLY! Specify
@@ -189,7 +200,7 @@ If the run was successful the most interesting files will be the RAxML files:
  - <outdir>/RAxML_bipartitions.final
  - <outdir>/RAxML_bootstrap.final
  - <outdir>/RAxML_info.final
-Further the log file (<outdir>/log) contains all executed commands and their output.
+Further the log file (<outdir>/bcgTree.log) contains all executed commands and their output.
 This is useful as a reference, for re-executing steps manually and for debugging in case something went wrong.
 All other files are the outputs of different steps of the pipeline.
 Their names should be self-explanatory.
@@ -218,47 +229,57 @@ Cliparts from [[openclipart.org]] have been used:
  - [[https://openclipart.org/detail/125869/diagramme-de-venn-venn-diagram][Venn Diagram]] ([[https://openclipart.org/share][CC-0/public domain]])
 The font is from [[fontlibrary.org]]:
  - [[https://fontlibrary.org/en/font/ranchers][Ranchers]] ([[http://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=OFL][SIL Open Font License]])
+
+** Related Tools
+
+These are some tools with similar goals and approaches. If you know another one, please open a pull request to add it to the list.
+
+ - [[https://github.com/jvollme/PO_2_MLSA][PO_2_MLSA]] - by [[https://github.com/jvollme][@jvollme]] - Enables the calculation of phylogenies based on single copy core genome gene products, based on bidirectional BLAST results obtained with proteinortho.
+ - [[https://www.ezbiocloud.net/tools/ubcg][UBCG]] - by Na, S. I., Kim, Y. O., Yoon, S. H., Ha, S. M., Baek, I. & Chun, J. (2018). UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56. [[https://doi.org/10.1007/s12275-018-8014-6][Paper]]
+
 ** Changes
-[[https://travis-ci.org/molbiodiv/bcgTree][https://travis-ci.org/molbiodiv/bcgTree.svg?branch=master]]
-*** v1.1.0 <2018-07-19 Do>
+[[https://github.com/molbiodiv/bcgTree/actions/workflows/test_perl.yml][https://github.com/molbiodiv/bcgTree/actions/workflows/test_perl.yml/badge.svg?branch=master]]
+*** v1.2.0 <2021-10-27>
+ - Add parameter ~--genome~ with translation via ~prodigal~ (#15)
+ - Update and improve documentation (#19, #35, #38, #44)
+ - Make GUI independent of working directory (#33)
+ - Switch CI from Travis to GitHub Actions (#45)
+*** v1.1.0 <2018-07-19>
  - Breaking: the default aa substitution model for RAxML changed from WAG to AUTO.
    This has an impact on performance (it is faster to set this parameter to a fixed value).
    To get the same behaviour as in earlier versions pass ~--raxml-aa-substitution-model=WAG~
  - Add parameter ~--raxml-aa-substitution-model~ (#29)
  - Add HMMs of [[https://www.ezbiocloud.net/tools/ubcg][UBCG]] (#25)
-*** v1.0.10 <2017-03-07 Di>
+*** v1.0.10 <2017-03-07>
  - Fix GUI, add scrollbar (#23)
  - Add parameter --raxml-args (#22)
-*** v1.0.9 <2017-03-03 Fr>
+*** v1.0.9 <2017-03-03>
  - Add parameters --min-proteomes and --all-proteomes (#21)
-*** v1.0.8 <2016-09-07 Mi>
+*** v1.0.8 <2016-09-07>
  - Set default bootstraps to 100
  - Add description for reproduction of results in paper
-*** v1.0.7 <2016-06-16 Do>
+*** v1.0.7 <2016-06-16>
  - Add logo to GUI
-*** v1.0.6 <2016-03-17 Do>
+*** v1.0.6 <2016-03-17>
  - Improve layout (avoid errors with large text fields)
  - Update jar file
-*** v1.0.5 <2016-03-17 Do>
+*** v1.0.5 <2016-03-17>
  - Add advanced settings and external programs to GUI
  - Add GUI screenshots to README
  - Finish GUI layout
  - Fix outdir bug (manually entered text was ignored)
  - Update documentation in README
  - Improve layout of GUI (proteomes panel)
-*** v1.0.4 <2016-02-23 Di>
+*** v1.0.4 <2016-02-23>
  - Add parameter to check external programs
  - Fix SeqFilter dependencies
  - Add swingx and own accordion element for GUI
  - Improve GUI design (GridBagLayout)
-*** v1.0.3 <2016-02-23 Di>
+*** v1.0.3 <2016-02-23>
  - Add log4perl and Getopt::ArgvFile to package (simplify installation)
-*** v1.0.2 <2016-02-22 Mo>
+*** v1.0.2 <2016-02-22>
  - Remove Bioperl dependency
  - Add submodules directly (SeqFilter)
  - Update documentation
-*** v1.0.1 <2016-02-22 Mo>
+*** v1.0.1 <2016-02-22>
  - Add java GUI
-
-** Fun
-See [[http://codeology.braintreepayments.com/molbiodiv/bcgtree][this visualization]] created by [[http://codeology.braintreepayments.com/][codeology]].