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NEWS.md

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Issues still to fix

  • for files with very long names I think R is truncating the file names for the pdf tree plot outputs. See (README.md)[README.md] for details

Fixes since v1.3.11

paml_wrapper_v1.3.11

  • docker container's R installation failed to install the ape package, so I got an error when trying to plot the trees. I think the newer ape package version available at CRAN probably fails to install on the very old version of R I have in the container. I fixed it by specifying an older version of ape, and by manually installing the Rcpp package rather than doing it as a dependency.

paml_wrapper_v1.3.10

  • more fixes to the pw_parsedPAMLconvertToWideFormat.pl script. Now assuming I'll mostly run in sbatch mode, on one gene at a time. If I need to combine results for pairs of CpG-masked and unmasked alignments, I'll make a different script to do that.

paml_wrapper_v1.3.9

  • tiny changes in pw_changenamesinphyliptreefile.pl to make it more useful outside the pipeline
  • changed pw_makeTreeAndRunPAML.pl to use --cpg=1 option when it calls the pw_parsedPAMLconvertToWideFormat.pl script. This fixes a situation whereby I was running PAML on a single CpG-masked alignment, and it produced an empty "wide" format output, because it didn't have the unmasked alignment to match the results up to.

paml_wrapper-v1.3.8

  • PAML 4.10.6 now requires tree files that contain an extra first line, but in paml_wrapper-v1.3.7, the --usertree option was broken for treefiles containing that extra first line. I've fixed that now.

paml_wrapper-v1.3.7

  • added an exit with error if there's only 1 seq in the alignment
  • added a test for alignments containing only 2 sequences (in which case PHYML tree building fails). I make a fake tree file ((seq1,seq2);) and proceed with PAML. Results are pretty much meaningless for the more complex models, but I think M0 versus M0fixed might still be useful
  • added the ability to run the scripts on input files that are not in the current directory. Output files goes where input file are.

paml_wrapper-v1.3.6

  • no longer build the bad 4.10.6 PAML versions in the docker container
  • remove the tarballs after compiling within the docker container, aiming for a smaller image
  • version 4.10.6 is now the default (compiled from github source, commit af30c37) in all scripts and in rhino/gizmo path
  • now not switching to --strict=loose for v4.10.6 (because it's not needed)

paml_wrapper-v1.3.5

  • now adding a first line (" numSeqs numTrees") to the tree input file for PAML, because newer codeml versions are more picky about tree format than the older versions were

paml_wrapper-v1.3.4

  • docker container now compiles a true v4.10.6 of PAML using PAML git repo commit af30c37 (Dec 1, 2022) (before I was using an out-of-date tarball that seemed like it was v4.10.6 but actually it wasn't)

paml_wrapper-v1.3.3

  • added smallDiff option to pw_makeTreeAndRunPAML.pl and to the sbatch and singularity wrappers

paml_wrapper-v1.3.2

  • Fixed tsv output so that every line has the same number of columns (displays better on github)

paml_wrapper-v1.3.1

Feb 10 2023, commit 61d7eee

  • minor changes, mostly cosmetic

paml_wrapper-v1.3.0

Feb 9 2023

  • added more PAML versions to the Docker container (4.9a, 4.9g, 4.9h, 4.9j, 4.10.6), to help me compare outputs from different versions. Specify which version to use with the option --version=4.9a (4.9a is the default)
  • added a --verbose=1 option to give me a bit more information in the PAMLsummary.tsv output file, to help with troubleshooting different results from different PAML versions

paml_wrapper-v1.2.2

Nov 23 2022, commit 34f462f

  • minor changes, mostly cosmetic

paml_wrapper-v1.2.1

Nov 23 2022, commit 33aa2c4

  • added --strict=loose option so that I can parse output of paml v4.10.6, because it does NOT print the 'Time used' message for M2 and M8 (the models where BEB is run)

Nov 23 2022, commit d889f42

  • now capturing elapsed time to the parsed output

Nov 23 2022, commit c1a9927

  • add --codeml option so that we can specify a different codeml executable. Useful for testing different versions of PAML. Not applicable when I'm running within singularity/docker: there I only installed a single version of PAML (currently 4.9j).

Nov 22 2022, commit 5f404a0

  • now capturing PAML version in parsed output

Nov 22 2022, commit 41b5282

  • now capturing tree file name in parsed output

paml_wrapper-v1.2.0

Nov 22 2022, commit 2354751

  • use PAML version 4.9j instead of 4.9a
  • total rebuild of the Docker/singularity container using bioperl-Ubuntu-trusty as a base rather than the original miniconda base. Couldn't install bioperl any more using conda. Wanted to rebuild so I could use PAML version 4.9j instead of 4.9a, and couldn't do that without also fixing the conda-bioperl problem

paml_wrapper-v1.1.0

Nov 16 2022, commit c0f6507

  • when using the --usertree option, we now check that the seqnames match up between the alignment and the tree, and offer some hints on what to do if they don't.

paml_wrapper-v1.0.9

Nov 15 2022, commit 2c3f9d0

  • added --usertree option to allow use of a user-specified tree (e.g. known species tree) rather than the default behavior of creating a tree from the alignment. For now I am not doing any checks on the tree, so there are ways this might break.

paml_wrapper-v1.0.8

Nov 1 2022, commit 974bf91

  • fixed a bug in pw_plottree.R that messed up taxon names when making pdf plots of the trees (does not affect PAML output, only the tree plots)
  • make the omega plots look a tiny bit nicer, and added clear indication on the plot that we're not showing the full range of omega in some cases
  • changed a column header in the tsv outputs: was 'seqToWhichSiteCoordsRefer', now 'seqToWhichAminoAcidsRefer'
  • running via singularity wrapper now records container version number in the log.txt file

paml_wrapper-v1.0.7

May 31 2022, commit f9e4bad

has known bug in pw_plottree.R that messed up taxon names when making pdf plots of the trees. don't use tree pdf files!

paml_wrapper-v1.0.6

May 5 2022

paml_wrapper-v1.0.5

May 4 2022

paml_wrapper-v1.0.4

May 3 2022

paml_wrapper-v1.0.3

April 28 2022

paml_wrapper-v1.0.2

April 28 2022