example files absent

[splaisan]

trying to run the example.sh, I get folder not found errors could it be that the files have been moved around? thanks

wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_R7_2D.fasta
--2019-06-06 10:56:57--  ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_R7_2D.fasta
           => ‘ecoli_R7_2D.fasta’
Resolving ftp.bcgsc.ca (ftp.bcgsc.ca)... 134.87.4.91
Connecting to ftp.bcgsc.ca (ftp.bcgsc.ca)|134.87.4.91|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /supplementary/NanoSim ... 
No such directory ‘supplementary/NanoSim’.

=> it seems the files are now @ http://www.bcgsc.ca/downloads/supplementary/NanoSim/ which could be corrected in the example.sh wget commands

[splaisan]

Similarly, the example.sh commands are obsolete and incorrect for the latest code version and can be replaced by something like this:

##### Inside NanoSim, create a working directory
mkdir ecoli_simulation
cd ecoli_simulation

# Get the 2D reads
wget http://www.bcgsc.ca/downloads/supplementary/NanoSim/ecoli_R7_2D.fasta

# Get the reference genome
wget http://www.bcgsc.ca/downloads/supplementary/NanoSim/ecoli_K12_MG1655_ref.fa

# Profiling stage (using a single thread, increase if you have more)
thr=1

../src/read_analysis.py genome -t ${thr} -i ecoli_R7_2D.fasta -r ecoli_K12_MG1655_ref.fa -o ecoli_R7_2D_model

# Simulation stage
../src/simulator.py genome -dna_type circular -rg ecoli_K12_MG1655_ref.fa -c ecoli_R7_2D_model -o R7_2D-simulated

[cheny19]

Hi @splaisan,

Thanks for bringing up this issue. Currently, we are undergoing major code merging and packaging. We will provide an example.sh file soon and release the next version of Nanosim. Stay tuned!

Thanks, Chen