summary from interop

[coykMccoyk]

Hello,
I’d like to get summary information from our NextSeq runs so I can look at performance across all our runs. I know the SAV software can do it per run, but I’d like to extract the summary table it gives for each of our runs. I’ve looked around Illumina’s github page. I’ve installed interop on our server using pip install interop. I’ve followed the directions here
http://illumina.github.io/interop/summary_table.html
is “summary” a command within interop? When I type
summary My/Run/File
on the command line, I get command not found.
I’ve also tried
interop My/Run/File
interop summary My/Run/File
python interop summary My/Run/File
Am I supposed to install something else? I copied the lines from
https://github.com/Illumina/interop/blob/master/docs/src/Tutorial_01_Intro.ipynb
into a single file
run_folder = r"/media/efglserv/seqspace/media/efglserv/seqspace/NextSeq/Runs/211222_NB501106_0401_AHT53TAFX2/"
from interop import py_interop_run_metrics, py_interop_run, py_interop_summary
run_metrics = py_interop_run_metrics.run_metrics()
valid_to_load = py_interop_run.uchar_vector(py_interop_run.MetricCount, 0)
py_interop_run_metrics.list_summary_metrics_to_load(valid_to_load)
run_folder = run_metrics.read(run_folder, valid_to_load)
summary = py_interop_summary.run_summary()
py_interop_summary.summarize_run_metrics(run_metrics, summary)
summary.total_summary().yield_g()
import pandas as pd
columns = ( ('Yield Total (G)', 'yield_g'), ('Projected Yield (G)', 'projected_yield_g'), ('% Aligned', 'percent_aligned'))
rows = [('Non-Indexed Total', summary.nonindex_summary()), ('Total', summary.total_summary())]
d = []
for label, func in columns:
d.append( (label, pd.Series([getattr(r[1], func)() for r in rows], index=[r[0] for r in rows])))
df = pd.DataFrame.from_items(d)
df

called the file Summaryinterops.py, then tried to run in from the command line using
python Summaryinterops.py
but got a bunch of error messages. I don’t know how to print the error messages to a file. It looks like it doesn’t like how I’ve specified the run folder and it can’t find "/media/efglserv/seqspace/media/efglserv/seqspace/NextSeq/Runs/211222_NB501106_0401_AHT53TAFX2/RunInfo.xml" though I can navigate to that folder and see that file there.

Any guidance would be appreciated. Also, did I really need to sign up for a github account to ask this question?

[ezralanglois]

The command line tools are stored by OS in:

Apple Mac: https://github.com/Illumina/interop/releases/download/v1.1.23/InterOp-1.1.23-Darwin-AppleClang.tar.gz
Linux: https://github.com/Illumina/interop/releases/download/v1.1.23/InterOp-1.1.23-Linux-GNU.tar.gz
Windows: https://github.com/Illumina/interop/releases/download/v1.1.23/InterOp-1.1.23-Windows-MSVC.zip

I suggest running

ls /media/efglserv/seqspace/media/efglserv/seqspace/NextSeq/Runs/211222_NB501106_0401_AHT53TAFX2/RunInfo.xml

If this does not work, then you have an issue on your side that I cannot help you with.

[coykMccoyk]

I've already installed interop on our server
After downloading from your link above, putting that on our server too I know have a folder
/home/efglserv/software/InterOp-1.1.23-Linux-Gnu
as well as what I installed using
pip install interop
Requirement already satisfied: numpy>=1.16 6 in /home/efglserv/anaconda3/lib/python3.6/site-packages (from interop) (1.18.5)

Still, when I type summary My/Run/Folder I get command not found.

In looking at the readme in InterOp-1.1.23-Linux-Gnu, there's a Python install section, which I've done, and a From Source section. Do I do that as well? Do I do the "Building with Interop GCC/Clang" part too?