-
Notifications
You must be signed in to change notification settings - Fork 342
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
starting off #55
Comments
Hi Martin, If you still get an error message from the command line you may not have git installed. If you don’t want to install git, you can alternatively download a zip file by using the “Clone or Download” button on the github page, selecting download zip, and unzipping that file. Cheers, On Jul 18, 2016, at 8:41 AM, mhsteppan notifications@github.com wrote:
|
Hi Raymond, |
Hi Martin, If you’re new to python the easiest solution is probably to install Anaconda, which comes with most of the major modules preconfigured and makes managing those dependencies much easier. Otherwise you’ll probably need to investigate python’s sys.path, your PATH and PYTHONPATH environment, and the location you install numpy to determine why python isn’t finding the module. Cheers, On Jul 21, 2016, at 5:34 AM, mhsteppan notifications@github.com wrote:
|
Hi! still having problems with the start. File "C:\Anaconda3\envs\py27\ldsc\ldsc.py", line 12, in I installed bitarray many times, using different methods, but it did not work. Can you help me with this problem. |
Hi Martin,
That’s odd, bitarray should be included in the base Anaconda installer, at least for current versions (check here: https://docs.continuum.io/anaconda/pkg-docs <https://docs.continuum.io/anaconda/pkg-docs>)
What versions of anaconda and python are you using? (i.e. output from running "python --version”)
Cheers,
Raymond
… On Nov 25, 2016, at 9:14 AM, mhsteppan ***@***.***> wrote:
Hi! still having problems with the start.
I get the following error message when trying to run: ldsc.py -h
File "C:\Anaconda3\envs\py27\ldsc\ldsc.py", line 12, in
import ldscore.ldscore as ld
File "C:\Anaconda3\envs\py27\ldsc\ldscore\ldscore.py", line 3, in
import bitarray as ba
ImportError: No module named bitarray
I installed bitarray many times, using different methods, but it did not work. Can you help me with this problem.
cheers,
martin
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub <#55 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AILEvWACVF3XWbHcB7SOkN3O4aPIYpZ8ks5rBu09gaJpZM4JOrF_>.
|
Hi Raymond, |
Hi Martin,
That is very strange. Unfortunately this is starting to sound like a local platform/working environment/configuration issue, which tends to be difficult to debug remotely. Do you happen to have local IT support who may be able to assist?
Cheers,
Raymond
… On Nov 30, 2016, at 4:13 AM, mhsteppan ***@***.***> wrote:
Hi Raymond,
I am using:
Python 2.7.12 :: Anaconda custom (64-bit)
The thing is that if I use "conda list" bitarray appears as installed.
Best,
Martin
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub <#55 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AILEvXOi9ik8yqGtc04gWAgTnVOpvF11ks5rDT4ugaJpZM4JOrF_>.
|
Hi Raymond,
it was a platform issue. I used another computer, where no python had been
installed, used anaconda python 2.7 and it worked :-)
There is just another little problem using the example code you provide on
the wiki. I always had to put "python" before the command. I also had to
put all the --options in one line, and I had to copy the .py files in the
working directory.
So the example code that worked for me was:
unzip -o pgc.cross.bip.zip
unzip -o pgc.cross.scz.zip
bunzip2 w_hm3.snplist.bz2
python munge_sumstats.py --sumstats pgc.cross.SCZ17.2013-05.txt --N 17115
--out scz --merge-alleles w_hm3.snplist
python munge_sumstats.py --sumstats pgc.cross.BIP11.2013-05.txt --N 11810
--out bip --merge-alleles w_hm3.snplist
python ldsc.py --rg scz.sumstats.gz,bip.sumstats.gz --ref-ld-chr
eur_w_ld_chr --w-ld-chr eur_w_ld_chr --out scz_bip
I had another problem with an external data source, but I ll open a new
thread on this topic...
cheers,
martin
2016-12-01 1:44 GMT+01:00 rkwalters <notifications@github.com>:
… Hi Martin,
That is very strange. Unfortunately this is starting to sound like a local
platform/working environment/configuration issue, which tends to be
difficult to debug remotely. Do you happen to have local IT support who may
be able to assist?
Cheers,
Raymond
> On Nov 30, 2016, at 4:13 AM, mhsteppan ***@***.***> wrote:
>
> Hi Raymond,
> I am using:
> Python 2.7.12 :: Anaconda custom (64-bit)
> The thing is that if I use "conda list" bitarray appears as installed.
> Best,
> Martin
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub <
#55 (comment)>, or mute
the thread <https://github.com/notifications/unsubscribe-auth/
AILEvXOi9ik8yqGtc04gWAgTnVOpvF11ks5rDT4ugaJpZM4JOrF_>.
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#55 (comment)>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/AIQfjNlXPZVjhGDvzhN8DeDmEWtG3pGyks5rDhhmgaJpZM4JOrF_>
.
|
Hi Martin, You're correct that the tutorial assumes that you are running you analyses in the same directory as the ldsc scripts. I'm surprised that the line breaks with '' between arguments were causing issues, so that's good to be aware of. I'll close this thread so we can focus on the other one. Thanks, |
hi! I have troubles starting with the first command:
git clone https://github.com/bulik/ldsc.git
this produces "invalid syntax" in all the python version I could find on the web.
do you know what this could be?
cheers,
martin
The text was updated successfully, but these errors were encountered: