David Studholme

circlator test fails at merge step

3

When I run circlator ```circlator test_output```, I get error messages at the merge step. It seems to be a problem with running nucmer: ```Running Circlator on test data... Made output...

SAMtools 1.15 is a more recent release than 1.3.

5

This issue is similar to, but distinct from issue #11. I have installed PhaME via conda and when I attempt to execute it, I get: `[13:18:16] Need samtools --version >=...

In [docs/quickstart.rst](https://github.com/widdowquinn/find_differential_primers/blob/diagnostic_primers/docs/quickstart.rst) section 1, there is the suggestion to install via conda with this command: `conda install -c bioconda pdp` However, bioconda does not contain any package called pdp. Bioconda...

I did git clone `https://github.com/widdowquinn/find_differential_primers` Here is the result of `git log | head`: ``` commit 54e4fb3d63d2610559d93249a5e389dad1caed90 Merge: 3e3863d cb830b4 Author: Leighton Pritchard Date: Fri Dec 18 14:20:49 2020 +0000...

I am using the tarball for the stable release v0.1.4 from here: [https://github.com/widdowquinn/find_differential_primers/archive/refs/tags/v0.1.4.tar.gz](https://github.com/widdowquinn/find_differential_primers/archive/refs/tags/v0.1.4.tar.gz). After doing `conda install --file requirements-thirdparty.txt` and `conda install --file requirements.txt`, I attempt to run the setup.py...

Failed to run with test data set: TypeError in line 45 of Snakefile

6

``` (base) ubuntu@bio-xanthomonas:~/dentist-example$ snakemake --configfile=snakemake.yml --use-singularity --cores=all Pre-fetching singularity image... TypeError in line 45 of /home/djs217/dentist-example/Snakefile: __init__() got an unexpected keyword argument 'is_containerized' File "/home/djs217/dentist-example/Snakefile", line 745, in File "/home/djs217/dentist-example/Snakefile",...