Cannot install

[liu-pinnng]

Hi,
I am keen on using bulkvis.
However, I can not install it.
While I try to run "pip install -r requirements.txt".
The following error will occure.

ERROR: Command errored out with exit status 1:
command: /Users/pingliu/envs/bulkvis/bin/python3 /Users/pingliu/envs/bulkvis/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/mz/4n1rp84s60j5p6mrh_7xgy5h0000gn/T/pip-build-env-wgn967th/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools Cython 'numpy==1.9.3; python_version=='"'"'3.5'"'"'' 'numpy==1.12.1; python_version=='"'"'3.6'"'"'' 'numpy==1.13.1; python_version>='"'"'3.7'"'"''
cwd: None
Complete output (4381 lines):
Ignoring numpy: markers 'python_version == "3.5"' don't match your environment
Ignoring numpy: markers 'python_version == "3.6"' don't match your environment
Collecting wheel
Using cached wheel-0.34.2-py2.py3-none-any.whl (26 kB)
Collecting setuptools
Using cached setuptools-47.3.1-py3-none-any.whl (582 kB)
Collecting Cython
Using cached Cython-0.29.20-cp37-cp37m-macosx_10_9_x86_64.whl (1.9 MB)
Collecting numpy==1.13.1
Using cached numpy-1.13.1.zip (5.0 MB)
Using legacy setup.py install for numpy, since package 'wheel' is not installed.
Installing collected packages: wheel, setuptools, Cython, numpy
Running setup.py install for numpy: started
Running setup.py install for numpy: still running...
Running setup.py install for numpy: finished with status 'error'

Can you help me to work out this problem.
Thank you in advance.

[alexomics]

Hi, the version of bulkvis on the master branch only works on python3.6 There is a newer release in development on branch 2.0 (5703700).

This second release works as a python package so can be installed like so:

~ pip install git+https://github.com/LooseLab/bulkvis.git@2.0

Then sub-commands are available using the bulkvis command:

~ bulkvis -h
usage: bulkvis [-h] [--version] {fuse,merge,serve,cite} ...

positional arguments:
  {fuse,merge,serve,cite}
                        Sub-commands
    fuse                Find incorrectly split reads from ONT
                        sequencing_summary.txt and minimap2 .paf files
    merge               Merge FASTQ files based on a fused_reads.txt or ONT
                        sequencing_summary.txt and minimap2 .paf files
    serve               Serve the bulk FAST5 file viewer web app
    cite                Output the citation for this tool and exit

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

See '<command> --help' to read about a specific sub-command.

[liu-pinnng]

Hi, Thank you for your reply and useful information. I will try it again. Best regards, Ping Liu alexomics <notifications@github.com> 於 2020年6月26日 週五 下午7:39寫道：

…

Hi, the version of bulkvis on the master branch only works on python3.6 There is a newer release in development on branch 2.0 (5703700 <5703700> ). This second release works as a python package so can be installed like so: ~ pip install ***@***.*** Then sub-commands are available using the bulkvis command: ~ bulkvis -h usage: bulkvis [-h] [--version] {fuse,merge,serve,cite} ... positional arguments: {fuse,merge,serve,cite} Sub-commands fuse Find incorrectly split reads from ONT sequencing_summary.txt and minimap2 .paf files merge Merge FASTQ files based on a fused_reads.txt or ONT sequencing_summary.txt and minimap2 .paf files serve Serve the bulk FAST5 file viewer web app cite Output the citation for this tool and exit optional arguments: -h, --help show this help message and exit --version show program's version number and exitSee '<command> --help' to read about a specific sub-command. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#40 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANHM3LOUGCET65ILF24WJYDRYR3H5ANCNFSM4OI33PFA> .

[liu-pinnng]

Hi, I set python version at 3.6.10 and installed the package as follows: Package Version

…

----------------- ------- bokeh 2.1.1 bulkvis 2.0.0a0 h5py 2.10.0 Jinja2 2.11.2 MarkupSafe 1.1.1 numpy 1.19.0 packaging 20.4 pandas 1.0.5 Pillow 7.2.0 pip 20.1.1 pyparsing 2.4.7 python-dateutil 2.8.1 pytz 2020.1 PyYAML 5.3.1 setuptools 40.6.2 six 1.15.0 tornado 6.0.4 tqdm 4.46.1 typing-extensions 3.7.4.2 wheel 0.34.2 However, when I am trying to run ‘bokeh serve --show bulkvis’ under envs file, the following error occurred: (bulkvis) PINGdeMacBook-Pro:envs pingliu$ bokeh serve --show bulkvis ERROR: No 'main.py' or 'main.ipynb' in /Users/pingliu/envs/bulkvis Could you tell me how to solve this problem? Thank you in advance! Best regards, Ping Liu 刘娉 <liuping930220@gmail.com> 於 2020年6月27日 週六 下午8:46寫道：

Hi, Thank you for your reply and useful information. I will try it again. Best regards, Ping Liu alexomics ***@***.***> 於 2020年6月26日 週五 下午7:39寫道： > Hi, the version of bulkvis on the master branch only works on python3.6 > There is a newer release in development on branch 2.0 (5703700 > <5703700> > ). > > This second release works as a python package so can be installed like so: > > ~ pip install ***@***.*** > > Then sub-commands are available using the bulkvis command: > > ~ bulkvis -h > usage: bulkvis [-h] [--version] {fuse,merge,serve,cite} ... > > positional arguments: > {fuse,merge,serve,cite} > Sub-commands > fuse Find incorrectly split reads from ONT > sequencing_summary.txt and minimap2 .paf files > merge Merge FASTQ files based on a fused_reads.txt or ONT > sequencing_summary.txt and minimap2 .paf files > serve Serve the bulk FAST5 file viewer web app > cite Output the citation for this tool and exit > > optional arguments: > -h, --help show this help message and exit > --version show program's version number and exitSee '<command> --help' to read about a specific sub-command. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#40 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ANHM3LOUGCET65ILF24WJYDRYR3H5ANCNFSM4OI33PFA> > . >

[alexomics]

To run the server:

bulkvis serve <BULK_FILE_DIRECTORY> --show

[liu-pinnng]

Thank you for quick response. After run 'bulkvis serve <BULK_FILE_DIRECTORY> --show' (bulkvis) PINGdeMacBook-Pro:envs pingliu$ bulkvis serve <BULK_FILE_DIRECTORY> --show

…

-bash: BULK_FILE_DIRECTORY: No such file or directory alexomics <notifications@github.com> 於 2020年7月1日 週三 下午9:44寫道：

To run the server: bulkvis serve <BULK_FILE_DIRECTORY> --show — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#40 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANHM3LNI6GEXQ42HD7JV2XDRZMVRHANCNFSM4OI33PFA> .

[alexomics]

Sorry, I wasn’t clear. You need to replace <BULK_FILE_DIRECTORY> with the path to your bulk FAST5 files

[liu-pinnng]

Thank you for your kind response☺️ I will try it. alexomics <notifications@github.com> 於 2020年7月1日 週三 下午10:04寫道：

…

Sorry, I wasn’t clear. You need to replace <BULK_FILE_DIRECTORY> with the path to your bulk FAST5 files — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#40 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANHM3LN6NRYEMPJOU3NV4KLRZMX5DANCNFSM4OI33PFA> .

[liu-pinnng]

Hi, I tried to replace <BULK_FILE_DIRECTORY> with the path to my bulk FAST5 files. However ... (bulkvis) (envs) PINGdeMacBook-Pro:envs pingliu$ bulkvis serve /Users/pingliu/envs/bulkvis/fast5files --show 2020-07-02 20:13:43,065 Starting Bokeh server version 2.1.1 (running on Tornado 6.0.4) 2020-07-02 20:13:43,068 Cannot start Bokeh server, port 5006 is already in use 刘娉 <liuping930220@gmail.com> 於 2020年7月1日 週三 下午10:52寫道：

…

Thank you for your kind response☺️ I will try it. alexomics ***@***.***> 於 2020年7月1日 週三 下午10:04寫道： > Sorry, I wasn’t clear. You need to replace <BULK_FILE_DIRECTORY> with > the path to your bulk FAST5 files > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#40 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ANHM3LN6NRYEMPJOU3NV4KLRZMX5DANCNFSM4OI33PFA> > . >

[alexomics]

So the port (5006) is already in use. You can set the server port using the port flag so your command should become:

bulkvis serve /Users/pingliu/envs/bulkvis/fast5files --show --port 5012

you can change the --port number to any open port