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Hi,
The following statement fails:
```
zcat fastqc_overrepresented_sequences.tsv.gz | python -m cgatcore.csv2db --retry --database-url=sqlite:///./csvdb --add-index=track --table=fastqc_ove…
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GIven the interest in studies that involve tumor heterogeneity / subclonality, currently bcbio offers "out of the box" support for both somatic variants and CNVs. A useful metric that can be combined …
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... might not be possible due to global pipeline dict
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Hello,
I installed cgatcore with:
```bash install-CGAT-tools.sh --devel --location /rds/general/project/medbio-berlanga-group/live/apps/bin/cgat_installation_2```
and ran the tests with:
```./in…
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Using OSX 10.14.1, I don't have brew installed and use ports(v2.5.4). I did try using brew and ports at one time which opened up a world of pain.
So i thought that using the python pip program was t…
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The issue is:
```
Downloading https://files.pythonhosted.org/packages/97/fe/12445c6793350ab5dbf76cb87a122b9e9aab9a9040a2801004806d985216/ruffus-2.6.3.tar.gz (36.9MB)
Complete output from co…
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Ocrmypdf is giving the following error on some b/w files:
```
ERROR - Traceback (most recent call last):
File "/usr/local/Cellar/ocrmypdf/5.6.2/libexec/lib/python3.6/site-packages/ruffus/task.py"…
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Hey there J,
I had a couple of PDFs which were segfaulting at specific pages. I think this still is an unresolved issue with tesseract. Please find the log below.
_________________________________…
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Due to the ruffus dependency, OCRmyPDF is incompatible with Python 3.7.
See https://github.com/cgat-developers/ruffus/pull/92
Given there has been no release of ruffus since 2015, it may be wort…
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Graphviz is no longer installed as part of the conda envs, and it is needed for ruffus to plot the pipeline, which, in turn is part of report building, even in reports where there is no longer a CGATR…