search

hiclib / pastis

Poisson-based algorithm for stable inference of DNA Structure
http://hiclib.github.io/pastis/
Other
34 stars 15 forks source link

Install/running problem- ./MDS.sh: 1: ./MDS.sh: MDS_all: not found #40

Open hanfu-bios opened 6 years ago

hanfu-bios commented 6 years ago

Hi,

I used python setup.py install --user to install the package on Unix. But I failed to run the examples. It gave me either ./MDS.sh: 1: ./MDS.sh: MDS_all: not found or pastis-mds: error: unrecognized arguments: -o -w 8 -r 10000 -k ./files/budding_yeast_structure -i ./wish_distances.txt -d -1 -c 1,2,3,4,5 -y 1

Any idea why? Do I need to install MDS_all and PM_all separately from the python package?

Thanks in advance.

Han

NelleV commented 6 years ago

Hi @hanfu-bios The recent releases do not use the compiled code "MDS_all" and "PM_all" anymore. There are several reasons why the code would still give errors. Do you mind answering the couple following questions?

  1. Where did you download the code from? It may be an old tarball.
  2. Did you have a previous installation of Pastis?

Many thanks,

hanfu-bios commented 6 years ago

Hi,

Thank you for your timely reply.

I downloaded the code from http://projets.cbio.mines-paristech.fr/~nvaroquaux/pastis/install.html http://projets.cbio.mines-paristech.fr/~nvaroquaux/pastis/install.html and also from the github page, they are in separate directories. I used the setup.py from the former webpage to install it since I cannot use pip in the server somehow. Should I use the setup file from github to install it?

I believe I have only installed it in the server once.

Thank you.

On Jul 4, 2018, at 1:28 PM, Nelle Varoquaux notifications@github.com wrote:

Hi @hanfu-bios https://github.com/hanfu-bios The recent releases do not use the compiled code "MDS_all" and "PM_all" anymore. There are several reasons why the code would still give errors. Do you mind answering the couple following questions?

Where did you download the code from? It may be an old tarball. Did you have a previous installation of Pastis? Many thanks,

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/hiclib/pastis/issues/40#issuecomment-402531141, or mute the thread https://github.com/notifications/unsubscribe-auth/Ad3Y_ZcDMu1_edt2Bp_gWG-BIuTb2d8zks5uDPsxgaJpZM4VCzPM.

NelleV commented 6 years ago

Hi @hanfu-bios I don't know what I did wrong, but the latest released tag on github does not correspond to the latest release, hence the problem… I'm investigating what happened right now, but in the mean time, can you update with this tarball? https://github.com/hiclib/pastis/archive/v0.3.0.zip Thanks

hanfu-bios commented 6 years ago

Hi,

I downloaded the package v0.3.0 from this link, installed the package via 'python setup.py install —user’. And then when I tried to run the examples, I received the following error:

Traceback (most recent call last): File "/usr/local/bin/pastis-mds", line 4, in from pastis.algorithms import run_mds File "/home/cai.507/.local/lib/python2.7/site-packages/pastis/algorithms.py", line 11, in from . import write ImportError: cannot import name write

Have you seen this before? Do you have any idea how to solve it?

Thanks a lot!

On Jul 4, 2018, at 1:58 PM, Nelle Varoquaux notifications@github.com wrote:

Hi @hanfu-bios https://github.com/hanfu-bios I don't know what I did wrong, but the latest released tag on github does not correspond to the latest release, hence the problem… I'm investigating what happened right now, but in the mean time, can you update with this tarball? https://github.com/hiclib/pastis/archive/v0.3.0.zip https://github.com/hiclib/pastis/archive/v0.3.0.zip Thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/hiclib/pastis/issues/40#issuecomment-402535465, or mute the thread https://github.com/notifications/unsubscribe-auth/Ad3Y_ZXWBfkYgm8RBNlIQzXLexANXykGks5uDQJTgaJpZM4VCzPM.

NelleV commented 6 years ago

Let me take a couple of hours to investigate what's going on on a fresh install.

NelleV commented 6 years ago

I believe that the now latest release should fix the problem. I broke the pip one though… https://github.com/hiclib/pastis/releases/tag/v0.3.1

Let me know if this doesn't work, and I'm terribly sorry about all of these troubles. I apparently broke my packaging recently…

hanfu-bios commented 6 years ago

Hi Nelle,

Thank you for the efforts for debugging the problems. I tried with this version, but the same error occurred as it did from the last version.

Traceback (most recent call last): File "/usr/local/bin/pastis-mds", line 4, in from pastis.algorithms import run_mds File "/home/cai.507/.local/lib/python2.7/site-packages/pastis/algorithms.py", line 11, in from . import write ImportError: cannot import name write

Do you have any idea what is going on here?

Thank you a lot!

Best, Han

On Jul 4, 2018, at 4:24 PM, Nelle Varoquaux notifications@github.com wrote:

I believe that the now latest release should fix the problem. I broke the pip one though… https://github.com/hiclib/pastis/releases/tag/v0.3.1 https://github.com/hiclib/pastis/releases/tag/v0.3.1 Let me know if this doesn't work, and I'm terribly sorry about all of these troubles. I apparently broke my packaging recently…

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/hiclib/pastis/issues/40#issuecomment-402554202, or mute the thread https://github.com/notifications/unsubscribe-auth/Ad3Y_YtqNLqiPDL4X6-GxvTaSVrCy5yQks5uDSSOgaJpZM4VCzPM.

NelleV commented 5 years ago

After a lot of fighting with packaging, I finally fixed all of the issues. if you reinstall or upgrade via pip, it should work ("pip install --upgrade"). Check that it downloads the 0.3.3 release, which I just released a couple of minutes ago, and it should be ok. It is possible that it takes a couple of hours for the servers to propagate this new release. Let me know if any other problems arise!

hanfu-bios commented 5 years ago

Nelle, thank you so much for your efforts! I can run the example right now, but I still have problems running my own data. I have attached my input files here. The error was

File "/Users/hanfu/.local/lib/python3.6/site-packages/pastis/externals/iced/filter.py", line 63, in filter_low_counts verbose=verbose) File "/Users/hanfu/.local/lib/python3.6/site-packages/pastis/externals/iced/filter.py", line 174, in _filter_low_sum X[X_sum < x, :] = np.nan ValueError: cannot convert float NaN to integer

Can you please help me by looking into this error?

Thanks a lot!