starting off

[mhsteppan]

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

[rkwalters]

Hi Martin, This command (and the rest of the tutorial) is intended to be run from the command line, not from within python.

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, Raymond

On Jul 18, 2016, at 8:41 AM, mhsteppan notifications@github.com wrote:

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

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[mhsteppan]

Hi Raymond, thank you very much. You can see I am a beginner with git. I also tried to install the requirements for LD SCore. However, when I run the second line in the tutorial: "./ldsc.py -h" after changing into the directory "ldsc" I get the error message: "ImportError: no module named numpy". do you know what I could do? cheers, martin

[rkwalters]

Hi Martin, Looks like you either don’t have the numpy python module installed, or python can’t find it from the search path.

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, Raymond

On Jul 21, 2016, at 5:34 AM, mhsteppan notifications@github.com wrote:

Hi Raymond, thank you very much. You can see I am a beginner with git. I also tried to install the requirements for LD SCore. However, when I run the second line in the tutorial: "./ldsc.py -h" after changing into the directory "ldsc" I get the error message: "ImportError: no module named numpy". do you know what I could do? cheers, martin

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[mhsteppan]

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

[rkwalters]

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 notifications@github.com 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

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[mhsteppan]

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

[rkwalters]

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 notifications@github.com 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

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[mhsteppan]

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 notifications@github.com 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

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[rkwalters]

Hi Martin, Glad you were able to get this working!

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, Raymond