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  • Mar 24 2016 17:46
    bmlewis-UCSD synchronize #107
  • Mar 15 2016 23:44
    apryan opened #130
  • Mar 15 2016 10:59
    anupriyatripathi opened #129
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    andersonbrookee synchronize #76
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  • Mar 07 2016 00:05
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ericsan119
@ericsan119
Screen Shot 2016-02-11 at 9.40.12 AM.png
Conall Sauvey
@csauvey
@olgabot when you had us make a "tscc" alias for sshing to the cluster, where was that? It's not in the .bashrc and I want to change it to always log in to login1
Alannah Miranda
@ahmirand
nano ~/.bash_profile
but before you login into tscc, so you can just command+T to open a new tab and do it there
Olga Botvinnik
@olgabot
@ericsan119 can you Uninstall and reinstall pandas?
I really don't know what's happening
ericsan119
@ericsan119
@olgabot What is the command for uninstalling and installing pandas on terminal ?
is it "pip uninstall pandas"?
ericsan119
@ericsan119
I did uninstall and install pandas. It still has not fixed...
ericsan119
@ericsan119
@olgabot I have fixed my problem. I just unchecked "Set locale environment variables on startup"
Screen Shot 2016-02-11 at 11.52.04 AM.png
Olga Botvinnik
@olgabot
@ericsan119 do conda uninstall pandas and conda install pandas instead of pip
because conda comes with all the C dependencies linked and pip doesn’t do that - pip is pure python
Olga Botvinnik
@olgabot
(video chat)
jk this one
bmlewis-UCSD
@bmlewis-UCSD
@olgabot where is S13_kallisto/abundance.tsv
when did 13 show up ? all I have is s10
Olga Botvinnik
@olgabot
You have to run Kallisto and featurecounts on both samples
That means you still need to run Kallisto on s13
bmlewis-UCSD
@bmlewis-UCSD
where is s13?
I have no idea
Olga Botvinnik
@olgabot
In the same place as s10
TThe same folder
bmlewis-UCSD
@bmlewis-UCSD
crying face
i am looking for that now
location should be in first s10.aligh.sh file?
Olga Botvinnik
@olgabot
Yeah
Or the Kallisto sh file
I showed in class that the folder contains a bunch of files
bmlewis-UCSD
@bmlewis-UCSD
k I just changed all the s10 to s13 s in the s10.align.sh and called it s13.align.sh and ran it
i just cd there
Olga Botvinnik
@olgabot
That works! That's what I did
bmlewis-UCSD
@bmlewis-UCSD
sigh
Olga Botvinnik
@olgabot
You can do it!
bmlewis-UCSD
@bmlewis-UCSD
thanks for the help, I am gonna take a mental health break , and try some more later
LElmen
@LElmen
@olgabot Hi Olga, for importing numpy & co, I opened python (otherwise it complains about syntax), it seems it imported correctly, but then for the next step "s10_kallisto = pd.read_table('S10_kallisto/abundance.tsv', index_col='target_id')" it keeps complaining about syntax, whether I'm in bash or python. I've tried changing the ' for " etc. I also tried "load pd". Any suggestions?
[ucsd-train05@tscc-login2 processed_data]$ s10_kallisto = pd.read_table('S10_kallisto/abundance.tsv', index_col="target_id"')
-bash: syntax error near unexpected token `('
Olga Botvinnik
@olgabot
Oh that should be run IN the jupyter notebook
It's python code so bash won't like it
LElmen
@LElmen
Aha... thank you
LElmen
@LElmen

I don't understand the # "_" is the previous output

assert _.index.shape == (17,)

What am i supposed to do here?
Olga Botvinnik
@olgabot
That's the solution checking code
The_ is the previous output
Olga Botvinnik
@olgabot
You don't have to do anything with it
Youtong Huang
@smugunicorn
I accidentally deleted everything in my processed_data folder... but when I tried to resubmit things in my processing_scripts (s10_kallisto.sh, s10_sort.sh, etc), my err files keep saying "Could not open a connection to your authentication agent." I suppose this may have something to do with ssh-add we have done in the beginning but I haven't figured out what to do with this error... Would you give me a clue on what to try?
Olga Botvinnik
@olgabot
I've seen that error on tscc sometimes, I think it's their fault not yours
Which queue are you submitting to?
Youtong Huang
@smugunicorn
hotel