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PAML installation from source #7

Merged
merged 22 commits into from
Apr 6, 2021
Merged

PAML installation from source #7

merged 22 commits into from
Apr 6, 2021

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Cecilia-Sensalari
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  • In containers PAML is now installed from source

  • Installation.rst updated for PAML local installation

  • Renamed "Paralog1" to "Ortholog1" in ortholog TSV file

  • Nextflow command is now without square brackets for the "-c" parameter

  • Lincense has now "ksrates" instead of "ks rate-correction"

@Cecilia-Sensalari
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Cecilia-Sensalari commented Mar 28, 2021 •
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Renaming "wgd" module to "wgd_ksrates":
We have called the wgd module integrated in ksrates simply "wgd", however this is also how wgd is called when installed separately (one might have wgd already installed or might want to install it later on). If for example you install first ksrates and then wgd, the most recent wgd will take over when "wgd" is called in the commands during our ksrates pipeline. This leads to some incompatibilities...
To solve this I'm giving a new name to our integrated wgd directory ("wgd_ksrates") and I'm changing it in the files where needed.

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lohausr commented Mar 31, 2021

Renaming "wgd" module to "wgd_ksrates":
We have called the wgd module integrated in ksrates simply "wgd", however this is also how wgd is called when installed separately (one might have wgd already installed or might want to install it later on). If for example you install first ksrates and then wgd, the most recent wgd will take over when "wgd" is called in the commands during our ksrates pipeline. This leads to some incompatibilities...
To solve this I'm giving a new name to our integrated wgd directory ("wgd_ksrates") and I'm changing it in the files where needed.

Hmm. We do not use the wgd command anywhere anymore, or do we? Is this also the case for the import statements, would it rather import from a separately installed wgd than the module integrated within ksrates?

lohausr
lohausr suggested changes Mar 31, 2021
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See a few edits and comments.

Dockerfile Outdated Show resolved Hide resolved
LICENSE Outdated
@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:

Ks Rate-Correction Copyright (C) 2020 Cecilia SENSALARI
ksrates Copyright (C) 2020 Cecilia SENSALARI
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Should probably be 2021. I know you did a lot of the coding, but I think any copyright should maybe at least go to both of us or the ESB lab instead.

LICENSE
Comment on lines 656 to 658
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
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We don't have any of those commands, this section would need to be adjusted.

Singularity
@@ -2,7 +2,7 @@ Bootstrap: docker
From: vibpsb/i-adhore
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Why this? Also in Dockerfile.

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doc/source/installation.rst Outdated
@@ -99,23 +100,41 @@ Without the use of a container the installation of *ksrates* and its dependencie
cd ksrates
pip3 install .

3. Non-Python dependencies can be installed in two possible ways.
3. Most of non-Python dependencies can be installed in two possible ways.
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Note that this is specific for Linux. Any suggestion for Windows? (I can add macOS later.)

doc/source/installation.rst Outdated Show resolved Hide resolved
doc/source/installation.rst Outdated Show resolved Hide resolved
doc/source/installation.rst Outdated Show resolved Hide resolved
ksrates/fc_wgd.py
@@ -383,6 +383,7 @@ def ks_orthologs(species1, species2, cds_fasta1, cds_fasta2, base_dir='.', eval_
if isinstance(results_df, type(None)) or results_df.empty:
logging.warning('No ortholog Ks data computed, will write empty ortholog Ks file!')
with open(os.path.join(output_dir, output_ks_file), 'w+') as o:
results_df = results_df.rename(columns={"Paralog1":"Ortholog1", "Paralog2":"Ortholog2"})
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It doesn't need any changes elsewhere, i.e. the column names are not read/used anywhere in our or wgd's code? Just making sure.

@Cecilia-Sensalari Cecilia-Sensalari merged commit 3798044 into master Apr 6, 2021
@Cecilia-Sensalari Cecilia-Sensalari deleted the container_paml branch April 8, 2021 09:46
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@Cecilia-Sensalari @lohausr