get an error when install

[wangmhan]

Hi,
I meet an error when install the velocyto.py: "Command "python setup.py egg_info" failed with error code 1".
How to fix it? I am not a super user on server.
Thanks!

[gioelelm]

Are you using a conda environment as in the instructions?

[wangmhan]

Hi, I install a local python with version 3.6.5, and it goes well as I used the way "install from source". After using the command: "pip install -e .", it print "Successfully installed velocyto". But when I try to run "velocyto --help", it turn out : velocyto: command not found. I have no idea what is wrong. 2018-06-26 16:13 GMT+02:00 Gioele La Manno <notifications@github.com>:

…

Are you using a conda environment as in the instructions? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#88 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AmuJ1j6jntBdPdT8dv6ikG36jG3mRNXdks5uAkGlgaJpZM4U37Md> .

[gioelelm]

I install a local python with version 3.6.5, and it goes well as I used the
way "install from source".

Sorry, but the problem is that you are not following instructions.

Independently of the way you install you need the right dependencies in place. Some of them (cython, numpy, scipy) include compiling C and fortran code and therefore the easiest way to install is to use conda. conda offers a very controlled and reproducible sandbox environment that does not touch your systems installation.

I am happy to help users with all problems related to software installation as soon as they follow the instructions and use conda for the dependencies installation. Otherwise I have no reference system and I don't feel like it is possible to help users effectively.... I could be dealing with all the kind of weird system related and python installation problems.

Please use conda and we will have this solved in a snap! Thanks

[slinnarsson]

Hi

You probably don't have tkinter installed. There may also be some more complex issue with X windows and the selection of matplotlib backends. We strongly recommend using Anaconda Python because it comes preinstalled with a large number of precompiled libraries and modules for scientific computing. Velocyto depends on many such libraries and you will need to install each one manually if you choose not to use conda.

I recommend starting over, with a fresh installation of Anaconda Python. It's easy to install, takes 5 mins, and does not require root access. It will install in your home directory. Once you have Anaconda Python, install velocyto according to the instructions and you should be all set!

[wangmhan]

Hi, Thank you. It indeed a problem with tkinter. So I follow your recommend to use Anaconda Python. After that, install velocyto successfully! BR 2018-06-26 17:04 GMT+02:00 Sten Linnarsson <notifications@github.com>:

…

Hi You probably don't have tkinter installed. There may also be some more complex issue with X windows and the selection of matplotlib backends. We strongly recommend using Anaconda Python <https://www.anaconda.com/downloads> because it comes preinstalled with a large number of precompiled libraries and modules for scientific computing. Velocyto depends on many such libraries and you will need to install each one manually if you choose not to use conda. I recommend starting over, with a fresh installation of Anaconda Python. It's easy to install, takes 5 mins, and does not require root access. It will install in your home directory. Once you have Anaconda Python, install velocyto according to the instructions and you should be all set! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#88 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AmuJ1qaK3hIcydi0Cmdao_YMWTTSDlG-ks5uAk2bgaJpZM4U37Md> .

[gioelelm]

:)

[MichaelPeibo]

@wangmhan Hi,
How do you fix it? I got same problem when install environment, when I tried to 'pip install pysam', I got the error report
Command "python setup.py egg_info" failed with error code 1"

and I check "tk" by conda list, "tk" did exist.

Any suggestion? Thanks!

Plus, I also tried install it in Mac, same error occurred.

PeibodeMacBook-Pro:~ peiboxu$ pip install pysam
Collecting pysam
Using cached https://files.pythonhosted.org/packages/f9/c4/f1b6963a05f415aa69c8efd64ebe460d56d03ecc75db70b0e8606b589ade/pysam-0.15.0.tar.gz
Complete output from command python setup.py egg_info:
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in /private/var/folders/tm/zqc192bn3vx5wcq3k_s743br0000gn/T/pip-install-0_m8ou09/pysam/htslib': configure: error: C compiler cannot create executables See config.log' for more details
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in /private/var/folders/tm/zqc192bn3vx5wcq3k_s743br0000gn/T/pip-install-0_m8ou09/pysam/htslib': configure: error: C compiler cannot create executables See config.log' for more details
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: None
Traceback (most recent call last):
File "", line 1, in
File "/private/var/folders/tm/zqc192bn3vx5wcq3k_s743br0000gn/T/pip-install-0_m8ou09/pysam/setup.py", line 223, in
htslib_make_options = run_make_print_config()
File "/private/var/folders/tm/zqc192bn3vx5wcq3k_s743br0000gn/T/pip-install-0_m8ou09/pysam/setup.py", line 69, in run_make_print_config
stdout = subprocess.check_output(["make", "-s", "print-config"])
File "/Users/peiboxu/anaconda3/lib/python3.6/subprocess.py", line 336, in check_output
**kwargs).stdout
File "/Users/peiboxu/anaconda3/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 1.

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/tm/zqc192bn3vx5wcq3k_s743br0000gn/T/pip-install-0_m8ou09/pysam/

[MichaelPeibo]

Hi, I did installed it in Mac,
it seems pysam has some compiling or other issues on Windows system, see pysam issue

Alternatively, I installed pysam by bioconda as suggested here
And also as suggested by previous issue
xcode-select --install and update gcc by conda install gcc

Finally, it worked. Cannot wait to try this method and my mac can carry it.

[wangmhan]

Hi, It is glad to know that you fixed it. I first installed it on the server, use their first recommendation which need to install anaconda before install the software. When I tried to install it on Mac, it is not smooth. It comes to many error, and I also search a long time for the solution. I think I fixed it with the cmd like: conda install gcc. MichaelPeibo <notifications@github.com> 于2018年9月10日周一 上午4:44写道：

…

Hi, I did installed it in Mac, it seems pysam has some compiling or other issues on Windows system, see pysam issue <pysam-developers/pysam#262> Alternatively, I installed pysam by bioconda as suggested here <pysam-developers/pysam#262 (comment)> And also as suggested by previous issue <#58> xcode-select --install and update gcc by conda install gcc Finally, it worked. Cannot wait to try this method and my mac can carry it. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#88 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AmuJ1qmtbFJJkSEDFhFPQVACcS-vw0Edks5uZdIRgaJpZM4U37Md> .

[brianpenghe]

I ran into the same error.
While I was trying to install it using conda, I realized that it can't be installed that way, according to your instruction here: http://velocyto.org/velocyto.py/install/index.html#install-using-conda
Any solutions?

[brianpenghe]

I ran into the same error.
While I was trying to install it using conda, I realized that it can't be installed that way, according to your instruction here: http://velocyto.org/velocyto.py/install/index.html#install-using-conda
Any solutions?

Actually I solved my own problem by typing:
conda install numpy scipy cython numba matplotlib scikit-learn h5py click