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Bioconda-precompiled prophyle_assembler is a major slowdown factor on newer macs

Status: Open.

#412 In prophyle/prophyle;

· karel-brinda opened on Apr 1, 2025

Propagation make clean – use xargs instead of -exec with find

Status: Open.

#398 In prophyle/prophyle;

· karel-brinda opened on Mar 14, 2024

Verify ProPhyle bioconda dependencies

Status: Open.

#395 In prophyle/prophyle;

· karel-brinda opened on Dec 7, 2023

Index propagation Makefile cannot deal with spaces in parental dirs

bug

cmd:index

Status: Open.

#376 In prophyle/prophyle;

· karel-brinda opened on May 18, 2022

Remove prophyle_index_footprint (redundant)

Status: Open.

#367 In prophyle/prophyle;

· karel-brinda opened on Aug 17, 2021

Use xopen for opening files

enhancement

Status: Open.

#366 In prophyle/prophyle;

· karel-brinda opened on Aug 16, 2021

When the number of input files is large, prophyle index check is too slow

Status: Open.

#355 In prophyle/prophyle;

· karel-brinda opened on Aug 9, 2021

Automatic autocompletion does weird things with the tree

bug

Status: Open.

#343 In prophyle/prophyle;

· karel-brinda opened on Jul 30, 2021

Manual compilation of BWA

bug

Status: Open.

#342 In prophyle/prophyle;

· karel-brinda opened on Mar 8, 2021

If a dataset fully contained, make a single fake sequence of legth 1

enhancement

Status: Open.

#341 In prophyle/prophyle;

· karel-brinda opened on Oct 14, 2020

Add times to logs in order to simply tuning on clusters

enhancement

Status: Open.

#339 In prophyle/prophyle;

· karel-brinda opened on Oct 10, 2020

Bacterial library contains archaeal genomes

bug

cmd:download

high importance

Status: Open.

#332 In prophyle/prophyle;

· nataquinones opened on Apr 10, 2019