Problem with installing Katuali #13

Sham397243 · 2020-10-15T02:48:31Z

Hi,
I tried to install Katuali program in ubuntu (https://releases.ubuntu.com/16.04/?_ga=2.229415391.231427745.1601872308-250255130.1599689398). After running the following commands, I still get the following Error 1 message when I try to “make install”. Please see the commands lines I have used bellow. Is this because I am using a different version of python? It would be great if someone can help.

Sudo apt install git
git clone https://github.com/nanoporetech/katuali.git
cd katuali
sudo apt install python3-venv python3-pip
python3 -m pip install –user virtualenv
make install
The message at the end
Makefile:21: recipe for target ‘install’ failed
Make: *** [install] Error 1

mwykes · 2020-10-19T09:02:57Z

Hi @Sham397243,
I just tried installing katuali on a new ubuntu16.04 docker image and it worked fine.
Could try installing again and save all the error messages to a file:

cd katuali
rm -rf venv
make install &>install.log

Then attach the install.log here?

Sham397243 · 2020-10-19T20:34:55Z

Hi, Thank you very much. I will save the error messages to a file and send you on Wednesday. Regards, @Sham397243<https://github.com/Sham397243> From: mwykes <notifications@github.com> Sent: Monday, 19 October 2020 8:03 PM To: nanoporetech/katuali <katuali@noreply.github.com> Cc: Abeynayake, Shamila <Shamila.Abeynayake@agriculture.gov.au>; Mention <mention@noreply.github.com> Subject: Re: [nanoporetech/katuali] Problem with installing Katuali (#13) [Marketing Mail] [SEC=UNCLASSIFIED] Hi @Sham397243<https://github.com/Sham397243>, I just tried installing katuali on a new ubuntu16.04 docker image and it worked fine. Could try installing again and save all the error messages to a file: cd katuali rm -rf venv make install &>install.log Then attach the install.log here? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#13 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARMFW7HXFHVBYA6A3Z3PITDSLP6FJANCNFSM4SRMKEBQ>.

…

------ IMPORTANT - This email and any attachments have been issued by the Australian Government Department of Agriculture, Water and the Environment. The material transmitted is for the use of the intended recipient only and may contain confidential, legally privileged, copyright or personal information. You should not copy, use or disclose it without authorisation from the Department. It is your responsibility to check any attachments for viruses and defects before opening or forwarding them. If you are not an intended recipient, please contact the sender of this email at once by return email and then delete both messages. Unintended recipients must not copy, use, disclose, rely on or publish this email or attachments. The Department of Agriculture, Water and the Environment is not liable for any loss or damage resulting from unauthorised use or dissemination of, or any reliance on, this email or attachments. If you have received this e-mail as part of a valid mailing list and no longer want to receive a message such as this one, advise the sender by return e-mail accordingly. This notice should not be deleted or altered ------

Sham397243 · 2020-10-21T03:24:08Z

Hi, Please find the attached install.log file. Regards, @Sham397243<https://github.com/Sham397243> From: Abeynayake, Shamila Sent: Tuesday, 20 October 2020 7:34 AM To: nanoporetech/katuali <reply@reply.github.com>; nanoporetech/katuali <katuali@noreply.github.com> Cc: Mention <mention@noreply.github.com> Subject: RE: [nanoporetech/katuali] Problem with installing Katuali (#13) [Marketing Mail] [SEC=UNCLASSIFIED] Hi, Thank you very much. I will save the error messages to a file and send you on Wednesday. Regards, @Sham397243<https://github.com/Sham397243> From: mwykes <notifications@github.com<mailto:notifications@github.com>> Sent: Monday, 19 October 2020 8:03 PM To: nanoporetech/katuali <katuali@noreply.github.com<mailto:katuali@noreply.github.com>> Cc: Abeynayake, Shamila <Shamila.Abeynayake@agriculture.gov.au<mailto:Shamila.Abeynayake@agriculture.gov.au>>; Mention <mention@noreply.github.com<mailto:mention@noreply.github.com>> Subject: Re: [nanoporetech/katuali] Problem with installing Katuali (#13) [Marketing Mail] [SEC=UNCLASSIFIED] Hi @Sham397243<https://github.com/Sham397243>, I just tried installing katuali on a new ubuntu16.04 docker image and it worked fine. Could try installing again and save all the error messages to a file: cd katuali rm -rf venv make install &>install.log Then attach the install.log here? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#13 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARMFW7HXFHVBYA6A3Z3PITDSLP6FJANCNFSM4SRMKEBQ>.

…

------ IMPORTANT - This email and any attachments have been issued by the Australian Government Department of Agriculture, Water and the Environment. The material transmitted is for the use of the intended recipient only and may contain confidential, legally privileged, copyright or personal information. You should not copy, use or disclose it without authorisation from the Department. It is your responsibility to check any attachments for viruses and defects before opening or forwarding them. If you are not an intended recipient, please contact the sender of this email at once by return email and then delete both messages. Unintended recipients must not copy, use, disclose, rely on or publish this email or attachments. The Department of Agriculture, Water and the Environment is not liable for any loss or damage resulting from unauthorised use or dissemination of, or any reliance on, this email or attachments. If you have received this e-mail as part of a valid mailing list and no longer want to receive a message such as this one, advise the sender by return e-mail accordingly. This notice should not be deleted or altered ------

mwykes · 2020-10-21T15:03:29Z

Hi @Sham397243, I can't see the file - could you try attaching the file (or copying it's contents) directly on github?

Sham397243 · 2020-10-21T23:10:34Z

Hi mwykes content of the saved file.

test -d venv || virtualenv venv --prompt '(katuali) ' --python=python3
created virtual environment CPython3.5.2.final.0-32 in 410ms
creator CPython3Posix(dest=/home/shamila/katuali/venv, clear=False, global=False)
seeder FromAppData(download=False, wheel=bundle, setuptools=bundle, pip=bundle, via=copy, app_data_dir=/home/shamila/.local/share/virtualenv)
added seed packages: pip==20.2.3, setuptools==50.3.0, wheel==0.35.1
activators XonshActivator,FishActivator,CShellActivator,BashActivator,PowerShellActivator,PythonActivator
. ./venv/bin/activate && pip install pip --upgrade
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Collecting pip
Downloading pip-20.2.4-py2.py3-none-any.whl (1.5 MB)
Installing collected packages: pip
Attempting uninstall: pip
Found existing installation: pip 20.2.3
Uninstalling pip-20.2.3:
Successfully uninstalled pip-20.2.3
Successfully installed pip-20.2.4
. ./venv/bin/activate && pip install -r requirements.txt
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Collecting drmaa
Using cached drmaa-0.7.9.tar.gz (30 kB)
Collecting gpustat
Using cached gpustat-0.6.0.tar.gz (78 kB)
Collecting pandas
Using cached pandas-0.24.2-cp35-cp35m-manylinux1_i686.whl (8.7 MB)
Collecting pysam==0.15.2
Using cached pysam-0.15.2.tar.gz (3.2 MB)
ERROR: Command errored out with exit status 1:
command: /home/shamila/katuali/venv/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ccaugk7u/pysam/setup.py'"'"'; file='"'"'/tmp/pip-install-ccaugk7u/pysam/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-f638vilg
cwd: /tmp/pip-install-ccaugk7u/pysam/
Complete output (118 lines):
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... no
checking for inflate in -lz... no
configure: error: zlib development files not found

HTSlib uses compression routines from the zlib library <http://zlib.net>.
Building HTSlib requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin)
is installed.

FAILED.  This error must be resolved in order to build HTSlib successfully.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... no
checking for inflate in -lz... no
configure: error: zlib development files not found

HTSlib uses compression routines from the zlib library <http://zlib.net>.
Building HTSlib requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin)
is installed.

FAILED.  This error must be resolved in order to build HTSlib successfully.
make[1]: ./version.sh: Command not found
make[1]: ./version.sh: Command not found
config.mk:2: *** Resolve configure error first.  Stop.
# pysam: no cython available - using pre-compiled C
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: None
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/tmp/pip-install-ccaugk7u/pysam/setup.py", line 223, in <module>
    htslib_make_options = run_make_print_config()
  File "/tmp/pip-install-ccaugk7u/pysam/setup.py", line 69, in run_make_print_config
    stdout = subprocess.check_output(["make", "-s", "print-config"])
  File "/usr/lib/python3.5/subprocess.py", line 626, in check_output
    **kwargs).stdout
  File "/usr/lib/python3.5/subprocess.py", line 708, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 2
----------------------------------------

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Makefile:16: recipe for target 'venv/bin/activate' failed
make: *** [venv/bin/activate] Error 1

Sham397243 · 2020-10-25T22:47:50Z

Hi mwykes, I have copied and pasted the content directly on github. Can you see the content now? Please let me know if you want me to attached the file again. Regards, Shamila. From: mwykes <notifications@github.com> Sent: Thursday, 22 October 2020 2:04 AM To: nanoporetech/katuali <katuali@noreply.github.com> Cc: Abeynayake, Shamila <Shamila.Abeynayake@agriculture.gov.au>; Mention <mention@noreply.github.com> Subject: Re: [nanoporetech/katuali] Problem with installing Katuali (#13) [Marketing Mail] [SEC=UNCLASSIFIED] Hi @Sham397243<https://github.com/Sham397243>, I can't see the file - could you try attaching the file (or copying it's contents) directly on github? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#13 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARMFW7FCCVMXRWELHGYDQGTSL3Z5HANCNFSM4SRMKEBQ>.

…

------ IMPORTANT - This email and any attachments have been issued by the Australian Government Department of Agriculture, Water and the Environment. The material transmitted is for the use of the intended recipient only and may contain confidential, legally privileged, copyright or personal information. You should not copy, use or disclose it without authorisation from the Department. It is your responsibility to check any attachments for viruses and defects before opening or forwarding them. If you are not an intended recipient, please contact the sender of this email at once by return email and then delete both messages. Unintended recipients must not copy, use, disclose, rely on or publish this email or attachments. The Department of Agriculture, Water and the Environment is not liable for any loss or damage resulting from unauthorised use or dissemination of, or any reliance on, this email or attachments. If you have received this e-mail as part of a valid mailing list and no longer want to receive a message such as this one, advise the sender by return e-mail accordingly. This notice should not be deleted or altered ------

mwykes · 2020-10-26T12:09:59Z

Hi @Sham397243,

The log file suggests that the error is occuring when pysam is being installed. For some reason, pip is trying to compile pysam from source, and then complains that some of the required libraries are missing.

Can you try installing pysam before running make install?

source venv/bin/activate
pip install --only-binary pysam pysam
make install

Sham397243 · 2020-10-28T01:38:30Z

Hi mwykes,
I have tried these steps, but still get the Error 1 message at the end. Please see the content below.

shamila@shamila-VirtualBox:$ ls
commands3.odt Desktop Documents Downloads examples.desktop Music Pictures Public Templates Videos
shamila@shamila-VirtualBox:$ sudo apt install git
[sudo] password for shamila:
Sorry, try again.
[sudo] password for shamila:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
git-man liberror-perl
Suggested packages:
git-daemon-run | git-daemon-sysvinit git-doc git-el git-email git-gui gitk gitweb git-arch git-cvs git-mediawiki
git-svn
The following NEW packages will be installed:
git git-man liberror-perl
0 to upgrade, 3 to newly install, 0 to remove and 79 not to upgrade.
Need to get 4,060 kB of archives.
After this operation, 28.2 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://au.archive.ubuntu.com/ubuntu xenial/main i386 liberror-perl all 0.17-1.2 [19.6 kB]
Get:2 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 git-man all 1:2.7.4-0ubuntu1.9 [736 kB]
Get:3 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 git i386 1:2.7.4-0ubuntu1.9 [3,304 kB]
Fetched 4,060 kB in 2s (1,600 kB/s)
Selecting previously unselected package liberror-perl.
(Reading database ... 215315 files and directories currently installed.)
Preparing to unpack .../liberror-perl_0.17-1.2_all.deb ...
Unpacking liberror-perl (0.17-1.2) ...
Selecting previously unselected package git-man.
Preparing to unpack .../git-man_1%3a2.7.4-0ubuntu1.9_all.deb ...
Unpacking git-man (1:2.7.4-0ubuntu1.9) ...
Selecting previously unselected package git.
Preparing to unpack .../git_1%3a2.7.4-0ubuntu1.9_i386.deb ...
Unpacking git (1:2.7.4-0ubuntu1.9) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up liberror-perl (0.17-1.2) ...
Setting up git-man (1:2.7.4-0ubuntu1.9) ...
Setting up git (1:2.7.4-0ubuntu1.9) ...
shamila@shamila-VirtualBox:$ ls
commands3.odt Desktop Documents Downloads examples.desktop Music Pictures Public Templates Videos
shamila@shamila-VirtualBox:$ ls
commands3.odt Desktop Documents Downloads examples.desktop Music Pictures Public Templates Videos
shamila@shamila-VirtualBox:$ git clone https://github.com/nanoporetech/katuali.git
Cloning into 'katuali'...
remote: Enumerating objects: 522, done.
remote: Counting objects: 100% (522/522), done.
remote: Compressing objects: 100% (268/268), done.
remote: Total 1172 (delta 276), reused 486 (delta 250), pack-reused 650
Receiving objects: 100% (1172/1172), 34.18 MiB | 2.70 MiB/s, done.
Resolving deltas: 100% (609/609), done.
Checking connectivity... done.
shamila@shamila-VirtualBox:$ ls
commands3.odt Desktop Documents Downloads examples.desktop katuali Music Pictures Public Templates Videos
shamila@shamila-VirtualBox:$ cd katuali
shamila@shamila-VirtualBox:/katuali$ sudo apt install python3-venv python3-pip
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
libexpat1-dev libpython3-dev libpython3.5-dev python-pip-whl python3-dev python3-setuptools python3-wheel
python3.5-dev python3.5-venv
Suggested packages:
python-setuptools-doc
The following NEW packages will be installed:
libexpat1-dev libpython3-dev libpython3.5-dev python-pip-whl python3-dev python3-pip python3-setuptools
python3-venv python3-wheel python3.5-dev python3.5-venv
0 to upgrade, 11 to newly install, 0 to remove and 79 not to upgrade.
Need to get 39.0 MB of archives.
After this operation, 53.2 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 libexpat1-dev i386 2.1.0-7ubuntu0.16.04.5 [115 kB]
Get:2 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 libpython3.5-dev i386 3.5.2-2ubuntu016.04.12 [37.1 MB]
Get:3 http://au.archive.ubuntu.com/ubuntu xenial/main i386 libpython3-dev i386 3.5.1-3 [6,968 B]
Get:4 http://au.archive.ubuntu.com/ubuntu xenial-updates/universe i386 python-pip-whl all 8.1.1-2ubuntu0.6 [1,112 kB]
Get:5 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 python3.5-dev i386 3.5.2-2ubuntu016.04.12 [413 kB]
Get:6 http://au.archive.ubuntu.com/ubuntu xenial/main i386 python3-dev i386 3.5.1-3 [1,198 B]
Get:7 http://au.archive.ubuntu.com/ubuntu xenial-updates/universe i386 python3-pip all 8.1.1-2ubuntu0.6 [109 kB]
Get:8 http://au.archive.ubuntu.com/ubuntu xenial/main i386 python3-setuptools all 20.7.0-1 [88.0 kB]
Get:9 http://au.archive.ubuntu.com/ubuntu xenial-updates/universe i386 python3.5-venv i386 3.5.2-2ubuntu016.04.12 [6,004 B]
Get:10 http://au.archive.ubuntu.com/ubuntu xenial/universe i386 python3-venv i386 3.5.1-3 [1,110 B]
Get:11 http://au.archive.ubuntu.com/ubuntu xenial/universe i386 python3-wheel all 0.29.0-1 [48.1 kB]
Fetched 39.0 MB in 17s (2,211 kB/s)
Selecting previously unselected package libexpat1-dev:i386.
(Reading database ... 216130 files and directories currently installed.)
Preparing to unpack .../libexpat1-dev_2.1.0-7ubuntu0.16.04.5_i386.deb ...
Unpacking libexpat1-dev:i386 (2.1.0-7ubuntu0.16.04.5) ...
Selecting previously unselected package libpython3.5-dev:i386.
Preparing to unpack .../libpython3.5-dev_3.5.2-2ubuntu016.04.12_i386.deb ...
Unpacking libpython3.5-dev:i386 (3.5.2-2ubuntu016.04.12) ...
Selecting previously unselected package libpython3-dev:i386.
Preparing to unpack .../libpython3-dev_3.5.1-3_i386.deb ...
Unpacking libpython3-dev:i386 (3.5.1-3) ...
Selecting previously unselected package python-pip-whl.
Preparing to unpack .../python-pip-whl_8.1.1-2ubuntu0.6_all.deb ...
Unpacking python-pip-whl (8.1.1-2ubuntu0.6) ...
Selecting previously unselected package python3.5-dev.
Preparing to unpack .../python3.5-dev_3.5.2-2ubuntu016.04.12_i386.deb ...
Unpacking python3.5-dev (3.5.2-2ubuntu016.04.12) ...
Selecting previously unselected package python3-dev.
Preparing to unpack .../python3-dev_3.5.1-3_i386.deb ...
Unpacking python3-dev (3.5.1-3) ...
Selecting previously unselected package python3-pip.
Preparing to unpack .../python3-pip_8.1.1-2ubuntu0.6_all.deb ...
Unpacking python3-pip (8.1.1-2ubuntu0.6) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../python3-setuptools_20.7.0-1_all.deb ...
Unpacking python3-setuptools (20.7.0-1) ...
Selecting previously unselected package python3.5-venv.
Preparing to unpack .../python3.5-venv_3.5.2-2ubuntu016.04.12_i386.deb ...
Unpacking python3.5-venv (3.5.2-2ubuntu016.04.12) ...
Selecting previously unselected package python3-venv.
Preparing to unpack .../python3-venv_3.5.1-3_i386.deb ...
Unpacking python3-venv (3.5.1-3) ...
Selecting previously unselected package python3-wheel.
Preparing to unpack .../python3-wheel_0.29.0-1_all.deb ...
Unpacking python3-wheel (0.29.0-1) ...
Processing triggers for doc-base (0.10.7) ...
Processing 1 added doc-base file...
Processing triggers for man-db (2.7.5-1) ...
Setting up libexpat1-dev:i386 (2.1.0-7ubuntu0.16.04.5) ...
Setting up libpython3.5-dev:i386 (3.5.2-2ubuntu016.04.12) ...
Setting up libpython3-dev:i386 (3.5.1-3) ...
Setting up python-pip-whl (8.1.1-2ubuntu0.6) ...
Setting up python3.5-dev (3.5.2-2ubuntu016.04.12) ...
Setting up python3-dev (3.5.1-3) ...
Setting up python3-pip (8.1.1-2ubuntu0.6) ...
Setting up python3-setuptools (20.7.0-1) ...
Setting up python3.5-venv (3.5.2-2ubuntu016.04.12) ...
Setting up python3-venv (3.5.1-3) ...
Setting up python3-wheel (0.29.0-1) ...
shamila@shamila-VirtualBox:/katuali$ python3 -m pip install --user virtualenv
Collecting virtualenv
Downloading https://files.pythonhosted.org/packages/97/f3/c064343ac58d1a54c393a3f66483a29500f644a5918deeb935d28673edd9/virtualenv-20.1.0-py2.py3-none-any.whl (4.9MB)
100% |████████████████████████████████| 4.9MB 249kB/s
Collecting appdirs<2,>=1.4.3 (from virtualenv)
Downloading https://files.pythonhosted.org/packages/3b/00/2344469e2084fb287c2e0b57b72910309874c3245463acd6cf5e3db69324/appdirs-1.4.4-py2.py3-none-any.whl
Collecting six<2,>=1.9.0 (from virtualenv)
Downloading https://files.pythonhosted.org/packages/ee/ff/48bde5c0f013094d729fe4b0316ba2a24774b3ff1c52d924a8a4cb04078a/six-1.15.0-py2.py3-none-any.whl
Collecting distlib<1,>=0.3.1 (from virtualenv)
Downloading https://files.pythonhosted.org/packages/f5/0a/490fa011d699bb5a5f3a0cf57de82237f52a6db9d40f33c53b2736c9a1f9/distlib-0.3.1-py2.py3-none-any.whl (335kB)
100% |████████████████████████████████| 337kB 1.5MB/s
Collecting importlib-metadata<3,>=0.12; python_version < "3.8" (from virtualenv)
Downloading https://files.pythonhosted.org/packages/6d/6d/f4bb28424bc677bce1210bc19f69a43efe823e294325606ead595211f93e/importlib_metadata-2.0.0-py2.py3-none-any.whl
Collecting importlib-resources>=1.0; python_version < "3.7" (from virtualenv)
Downloading https://files.pythonhosted.org/packages/24/05/d81725e24bf6028a5753d2eab67d4ee7d8a20a793125727bf87f85e8dffc/importlib_resources-3.2.0-py2.py3-none-any.whl
Collecting filelock<4,>=3.0.0 (from virtualenv)
Downloading https://files.pythonhosted.org/packages/93/83/71a2ee6158bb9f39a90c0dea1637f81d5eef866e188e1971a1b1ab01a35a/filelock-3.0.12-py3-none-any.whl
Collecting zipp>=0.5 (from importlib-metadata<3,>=0.12; python_version < "3.8"->virtualenv)
Downloading https://files.pythonhosted.org/packages/41/ad/6a4f1a124b325618a7fb758b885b68ff7b058eec47d9220a12ab38d90b1f/zipp-3.4.0-py3-none-any.whl
Installing collected packages: appdirs, six, distlib, zipp, importlib-metadata, importlib-resources, filelock, virtualenv
Successfully installed appdirs distlib filelock importlib-metadata importlib-resources six-1.10.0 virtualenv zipp
You are using pip version 8.1.1, however version 20.2.4 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
shamila@shamila-VirtualBox:/katuali$ source venv/bin/activate
bash: venv/bin/activate: No such file or directory
shamila@shamila-VirtualBox:/katuali$ pip install --only-binary pysam pysam
The program 'pip' is currently not installed. You can install it by typing:
sudo apt install python-pip
shamila@shamila-VirtualBox:/katuali$ sudo apt install python-pip
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
libpython-all-dev libpython-dev libpython2.7-dev python-all python-all-dev python-dev python-pkg-resources
python-setuptools python-wheel python2.7-dev
Suggested packages:
python-setuptools-doc
The following NEW packages will be installed:
libpython-all-dev libpython-dev libpython2.7-dev python-all python-all-dev python-dev python-pip
python-pkg-resources python-setuptools python-wheel python2.7-dev
0 to upgrade, 11 to newly install, 0 to remove and 79 not to upgrade.
Need to get 28.4 MB of archives.
After this operation, 39.8 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 libpython2.7-dev i386 2.7.12-1ubuntu016.04.13 [27.7 MB]
Get:2 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 libpython-dev i386 2.7.12-116.04 [7,850 B]
Get:3 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 libpython-all-dev i386 2.7.12-116.04 [1,006 B]
Get:4 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 python-all i386 2.7.12-116.04 [986 B]
Get:5 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 python2.7-dev i386 2.7.12-1ubuntu016.04.13 [276 kB]
Get:6 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 python-dev i386 2.7.12-116.04 [1,174 B]
Get:7 http://au.archive.ubuntu.com/ubuntu xenial-updates/main i386 python-all-dev i386 2.7.12-116.04 [1,012 B]
Get:8 http://au.archive.ubuntu.com/ubuntu xenial-updates/universe i386 python-pip all 8.1.1-2ubuntu0.6 [144 kB]
Get:9 http://au.archive.ubuntu.com/ubuntu xenial/main i386 python-pkg-resources all 20.7.0-1 [108 kB]
Get:10 http://au.archive.ubuntu.com/ubuntu xenial/main i386 python-setuptools all 20.7.0-1 [169 kB]
Get:11 http://au.archive.ubuntu.com/ubuntu xenial/universe i386 python-wheel all 0.29.0-1 [48.0 kB]
Fetched 28.4 MB in 12s (2,348 kB/s)
Selecting previously unselected package libpython2.7-dev:i386.
(Reading database ... 216534 files and directories currently installed.)
Preparing to unpack .../libpython2.7-dev_2.7.12-1ubuntu016.04.13_i386.deb ...
Unpacking libpython2.7-dev:i386 (2.7.12-1ubuntu016.04.13) ...
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Unpacking libpython-dev:i386 (2.7.12-116.04) ...
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Unpacking libpython-all-dev:i386 (2.7.12-116.04) ...
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Preparing to unpack .../python-all_2.7.12-116.04_i386.deb ...
Unpacking python-all (2.7.12-116.04) ...
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Unpacking python2.7-dev (2.7.12-1ubuntu016.04.13) ...
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shamila@shamila-VirtualBox:/katuali$ source venv/bin/activate
bash: venv/bin/activate: No such file or directory
shamila@shamila-VirtualBox:/katuali$ pip install --only-binary pysam pysam
Collecting pysam
Could not find a version that satisfies the requirement pysam (from versions: )
No matching distribution found for pysam
You are using pip version 8.1.1, however version 20.2.4 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
shamila@shamila-VirtualBox:/katuali$ source venv/bin/activate
bash: venv/bin/activate: No such file or directory
shamila@shamila-VirtualBox:/katuali$ pip install --upgrade pip
Collecting pip
Downloading https://files.pythonhosted.org/packages/cb/28/91f26bd088ce8e22169032100d4260614fc3da435025ff389ef1d396a433/pip-20.2.4-py2.py3-none-any.whl (1.5MB)
100% |████████████████████████████████| 1.5MB 447kB/s
Installing collected packages: pip
Successfully installed pip-8.1.1
You are using pip version 8.1.1, however version 20.2.4 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
shamila@shamila-VirtualBox:/katuali$ pip install --only-binary pysam pysam
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see pypa/pip#5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Defaulting to user installation because normal site-packages is not writeable
Collecting pysam
Downloading pysam-0.15.4-cp27-cp27mu-manylinux2010_i686.whl (7.7 MB)
|████████████████████████████████| 7.7 MB 3.5 MB/s
Installing collected packages: pysam
Successfully installed pysam-0.15.4
shamila@shamila-VirtualBox:/katuali$ source venv/bin/activate
bash: venv/bin/activate: No such file or directory
shamila@shamila-VirtualBox:~/katuali$ make install
test -d venv || virtualenv venv --prompt '(katuali) ' --python=python3
created virtual environment CPython3.5.2.final.0-32 in 1872ms
creator CPython3Posix(dest=/home/shamila/katuali/venv, clear=False, global=False)
seeder FromAppData(download=False, wheel=bundle, pip=bundle, setuptools=bundle, via=copy, app_data_dir=/home/shamila/.local/share/virtualenv)
added seed packages: pip==20.2.4, setuptools==50.3.2, wheel==0.35.1
activators BashActivator,XonshActivator,PythonActivator,CShellActivator,FishActivator,PowerShellActivator
. ./venv/bin/activate && pip install pip --upgrade
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already up-to-date: pip in ./venv/lib/python3.5/site-packages (20.2.4)
. ./venv/bin/activate && pip install -r requirements.txt
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Collecting drmaa
Downloading drmaa-0.7.9.tar.gz (30 kB)
Collecting gpustat
Downloading gpustat-0.6.0.tar.gz (78 kB)
|████████████████████████████████| 78 kB 1.6 MB/s
Collecting pandas
Downloading pandas-0.24.2-cp35-cp35m-manylinux1_i686.whl (8.7 MB)
|████████████████████████████████| 8.7 MB 3.0 MB/s
Collecting pysam==0.15.2
Downloading pysam-0.15.2.tar.gz (3.2 MB)
|████████████████████████████████| 3.2 MB 4.0 MB/s
ERROR: Command errored out with exit status 1:
command: /home/shamila/katuali/venv/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-iuu291p9/pysam/setup.py'"'"'; file='"'"'/tmp/pip-install-iuu291p9/pysam/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-ibi92nxg
cwd: /tmp/pip-install-iuu291p9/pysam/
Complete output (118 lines):
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... no
checking for inflate in -lz... no
configure: error: zlib development files not found

HTSlib uses compression routines from the zlib library <http://zlib.net>.
Building HTSlib requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin)
is installed.

FAILED.  This error must be resolved in order to build HTSlib successfully.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... no
checking for inflate in -lz... no
configure: error: zlib development files not found

HTSlib uses compression routines from the zlib library <http://zlib.net>.
Building HTSlib requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin)
is installed.

FAILED.  This error must be resolved in order to build HTSlib successfully.
make[1]: ./version.sh: Command not found
make[1]: ./version.sh: Command not found
config.mk:2: *** Resolve configure error first.  Stop.
# pysam: no cython available - using pre-compiled C
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: None
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/tmp/pip-install-iuu291p9/pysam/setup.py", line 223, in <module>
    htslib_make_options = run_make_print_config()
  File "/tmp/pip-install-iuu291p9/pysam/setup.py", line 69, in run_make_print_config
    stdout = subprocess.check_output(["make", "-s", "print-config"])
  File "/usr/lib/python3.5/subprocess.py", line 626, in check_output
    **kwargs).stdout
  File "/usr/lib/python3.5/subprocess.py", line 708, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 2
----------------------------------------

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Makefile:16: recipe for target 'venv/bin/activate' failed
make: *** [venv/bin/activate] Error 1
shamila@shamila-VirtualBox:/katuali$ python3 -m venv path/to/venv
shamila@shamila-VirtualBox:/katuali$ source venv/bin/activate
(katuali) shamila@shamila-VirtualBox:~/katuali$ make install
. ./venv/bin/activate && python setup.py develop
running develop
running egg_info
creating katuali.egg-info
writing top-level names to katuali.egg-info/top_level.txt
writing dependency_links to katuali.egg-info/dependency_links.txt
writing katuali.egg-info/PKG-INFO
writing entry points to katuali.egg-info/entry_points.txt
writing requirements to katuali.egg-info/requires.txt
writing manifest file 'katuali.egg-info/SOURCES.txt'
reading manifest file 'katuali.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'build'
no previously-included directories found matching 'docs'
writing manifest file 'katuali.egg-info/SOURCES.txt'
running build_ext
Creating /home/shamila/katuali/venv/lib/python3.5/site-packages/katuali.egg-link (link to .)
Adding katuali 0.3.2 to easy-install.pth file
Installing katuali_datafile script to /home/shamila/katuali/venv/bin
Installing pick_gpu script to /home/shamila/katuali/venv/bin
Installing katuali_config script to /home/shamila/katuali/venv/bin
Installing process_katuali_config script to /home/shamila/katuali/venv/bin
Installing check_files_exist script to /home/shamila/katuali/venv/bin
Installing katuali script to /home/shamila/katuali/venv/bin

Installed /home/shamila/katuali
Processing dependencies for katuali==0.3.2
Searching for snakemake==5.9.1
Reading https://pypi.org/simple/snakemake/
Downloading https://files.pythonhosted.org/packages/53/39/5aa24036770e65c7d9bfb5ac99621e76cad9a0785d8f5ffc0124cebf28d1/snakemake-5.9.1.tar.gz#sha256=ff06e4e789b40eb52fc7fca3abcfcc3eeafa07acfe78d45791b7e39dfe2d7e68
Best match: snakemake 5.9.1
Processing snakemake-5.9.1.tar.gz
Writing /tmp/easy_install-egwzixj6/snakemake-5.9.1/setup.cfg
Running snakemake-5.9.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-egwzixj6/snakemake-5.9.1/egg-dist-tmp-ronmw01w
UPDATING build/lib/snakemake/_version.py
set build/lib/snakemake/_version.py to '5.9.1'
creating /home/shamila/katuali/venv/lib/python3.5/site-packages/snakemake-5.9.1-py3.5.egg
Extracting snakemake-5.9.1-py3.5.egg to /home/shamila/katuali/venv/lib/python3.5/site-packages
Adding snakemake 5.9.1 to easy-install.pth file
Installing snakemake script to /home/shamila/katuali/venv/bin
Installing snakemake-bash-completion script to /home/shamila/katuali/venv/bin

Installed /home/shamila/katuali/venv/lib/python3.5/site-packages/snakemake-5.9.1-py3.5.egg
Searching for pysam==0.15.2
Reading https://pypi.org/simple/pysam/
Downloading https://files.pythonhosted.org/packages/15/f6/ce0611aaa1865a616f7dc164fbf046eaf38f2b17c6d404403c56250beb93/pysam-0.15.2.tar.gz#sha256=d049efd91ed5b1af515aa30280bc9cb46a92ddd15d546c9b21ee68a6ed4055d9
Best match: pysam 0.15.2
Processing pysam-0.15.2.tar.gz
Writing /tmp/easy_install-vr1yulrj/pysam-0.15.2/setup.cfg
Running pysam-0.15.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-vr1yulrj/pysam-0.15.2/egg-dist-tmp-7hkq4dxo

pysam: no cython available - using pre-compiled C

pysam: htslib mode is shared

pysam: HTSLIB_CONFIGURE_OPTIONS=None

checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... no
checking for inflate in -lz... no
configure: error: zlib development files not found

HTSlib uses compression routines from the zlib library http://zlib.net.
Building HTSlib requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin)
is installed.

FAILED. This error must be resolved in order to build HTSlib successfully.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... no
checking for inflate in -lz... no
configure: error: zlib development files not found

HTSlib uses compression routines from the zlib library http://zlib.net.
Building HTSlib requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin)
is installed.

FAILED. This error must be resolved in order to build HTSlib successfully.

pysam: htslib configure options: None

make[1]: ./version.sh: Command not found
make[1]: ./version.sh: Command not found
config.mk:2: *** Resolve configure error first. Stop.
Traceback (most recent call last):
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 152, in save_modules
yield saved
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 193, in setup_context
yield
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 254, in run_setup
_execfile(setup_script, ns)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 43, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-vr1yulrj/pysam-0.15.2/setup.py", line 223, in
File "/tmp/easy_install-vr1yulrj/pysam-0.15.2/setup.py", line 69, in run_make_print_config
'check_files_exist = {}:check_files_exist'.format(pkg_name),
File "/usr/lib/python3.5/subprocess.py", line 626, in check_output
**kwargs).stdout
File "/usr/lib/python3.5/subprocess.py", line 708, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 2

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "setup.py", line 77, in
os.path.join('scripts', x) for x in ('katuali',)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/init.py", line 153, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.5/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.5/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/command/develop.py", line 34, in run
self.install_for_development()
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/command/develop.py", line 151, in install_for_development
self.process_distribution(None, self.dist, not self.no_deps)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 742, in process_distribution
[requirement], self.local_index, self.easy_install
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/pkg_resources/init.py", line 766, in resolve
replace_conflicting=replace_conflicting
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/pkg_resources/init.py", line 1049, in best_match
return self.obtain(req, installer)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/pkg_resources/init.py", line 1061, in obtain
return installer(requirement)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 669, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 695, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 880, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 1150, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 1134, in run_setup
run_setup(setup_script, args)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 257, in run_setup
raise
File "/usr/lib/python3.5/contextlib.py", line 77, in exit
self.gen.throw(type, value, traceback)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 193, in setup_context
yield
File "/usr/lib/python3.5/contextlib.py", line 77, in exit
self.gen.throw(type, value, traceback)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 164, in save_modules
saved_exc.resume()
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 139, in resume
raise exc.with_traceback(self._tb)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 152, in save_modules
yield saved
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 193, in setup_context
yield
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 254, in run_setup
_execfile(setup_script, ns)
File "/home/shamila/katuali/venv/lib/python3.5/site-packages/setuptools/sandbox.py", line 43, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-vr1yulrj/pysam-0.15.2/setup.py", line 223, in
File "/tmp/easy_install-vr1yulrj/pysam-0.15.2/setup.py", line 69, in run_make_print_config
'check_files_exist = {}:check_files_exist'.format(pkg_name),
File "/usr/lib/python3.5/subprocess.py", line 626, in check_output
**kwargs).stdout
File "/usr/lib/python3.5/subprocess.py", line 708, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 2
Makefile:21: recipe for target 'install' failed
make: *** [install] Error 1
(katuali) shamila@shamila-VirtualBox:~/katuali$

mwykes · 2020-10-28T08:08:24Z

It looks like you are using the i686 32bit version of Ubuntu. As there are no i686 wheels for Pysam, pip resorts to building from source. We have never installed or tested Katuali on a 32bit OS, and as such we cannot support this. If you can install the x86 64-bit version of Ubuntu, this will make installing katuali and all of the katuali dependencies straightforward.

Sham397243 · 2020-10-29T01:18:38Z

Thank you very much. I will give a try with x86 64-bit version of Ubuntu.

Sham397243 · 2020-11-12T02:08:17Z

Hi mwykes, Now I have installed the correct version of ubuntu. What is the command I should use to install correct version of python? Please see below. I would like to have your opinion from this point. Regards, Shamila. To run a command as administrator (user "root"), use "sudo <command>". See "man sudo_root" for details. shamila@shamila-VirtualBox:~$ git clone https://github.com/nanoporetech/katuali.git The program 'git' is currently not installed. You can install it by typing: sudo apt install git shamila@shamila-VirtualBox:~$ sudo apt install git [sudo] password for shamila: Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: git-man liberror-perl Suggested packages: git-daemon-run | git-daemon-sysvinit git-doc git-el git-email git-gui gitk gitweb git-arch git-cvs git-mediawiki git-svn The following NEW packages will be installed: git git-man liberror-perl 0 to upgrade, 3 to newly install, 0 to remove and 119 not to upgrade. Need to get 3,932 kB of archives. After this operation, 25.6 MB of additional disk space will be used. Do you want to continue? [Y/n] y Get:1 http://au.archive.ubuntu.com/ubuntu xenial/main amd64 liberror-perl all 0.17-1.2 [19.6 kB] Get:2 http://au.archive.ubuntu.com/ubuntu xenial-updates/main amd64 git-man all 1:2.7.4-0ubuntu1.9 [736 kB] Get:3 http://au.archive.ubuntu.com/ubuntu xenial-updates/main amd64 git amd64 1:2.7.4-0ubuntu1.9 [3,176 kB] Fetched 3,932 kB in 4s (850 kB/s) Selecting previously unselected package liberror-perl. (Reading database ... 178110 files and directories currently installed.) Preparing to unpack .../liberror-perl_0.17-1.2_all.deb ... Unpacking liberror-perl (0.17-1.2) ... Selecting previously unselected package git-man. Preparing to unpack .../git-man_1%3a2.7.4-0ubuntu1.9_all.deb ... Unpacking git-man (1:2.7.4-0ubuntu1.9) ... Selecting previously unselected package git. Preparing to unpack .../git_1%3a2.7.4-0ubuntu1.9_amd64.deb ... Unpacking git (1:2.7.4-0ubuntu1.9) ... Processing triggers for man-db (2.7.5-1) ... Setting up liberror-perl (0.17-1.2) ... Setting up git-man (1:2.7.4-0ubuntu1.9) ... Setting up git (1:2.7.4-0ubuntu1.9) ... shamila@shamila-VirtualBox:~$ git clone https://github.com/nanoporetech/katuali.git Cloning into 'katuali'... remote: Enumerating objects: 522, done. remote: Counting objects: 100% (522/522), done. remote: Compressing objects: 100% (268/268), done. remote: Total 1172 (delta 276), reused 486 (delta 250), pack-reused 650 Receiving objects: 100% (1172/1172), 34.18 MiB | 1.74 MiB/s, done. Resolving deltas: 100% (609/609), done. Checking connectivity... done. shamila@shamila-VirtualBox:~$ ls Desktop Downloads katuali Pictures Templates Documents examples.desktop Music Public Videos shamila@shamila-VirtualBox:~$ cd katuali shamila@shamila-VirtualBox:~/katuali$ make install test -d venv || virtualenv venv --prompt '(katuali) ' --python=python3 /bin/sh: 1: virtualenv: not found Makefile:16: recipe for target 'venv/bin/activate' failed make: *** [venv/bin/activate] Error 127 shamila@shamila-VirtualBox:~/katuali$ From: mwykes <notifications@github.com> Sent: Wednesday, 28 October 2020 7:09 PM To: nanoporetech/katuali <katuali@noreply.github.com> Cc: Abeynayake, Shamila <Shamila.Abeynayake@agriculture.gov.au>; Mention <mention@noreply.github.com> Subject: Re: [nanoporetech/katuali] Problem with installing Katuali (#13) [Marketing Mail] [SEC=UNCLASSIFIED] It looks like you are using the i686 32bit version of Ubuntu. As there are no i686 wheels for Pysam, pip resorts to building from source. We have never installed or tested Katuali on a 32bit OS, and as such we cannot support this. If you can install the x86 64-bit version of Ubuntu, this will make installing katuali and all of the katuali dependencies<https://nanoporetech.github.io/katuali/installation.html#dependencies> straightforward. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#13 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARMFW7DXTEISO6VZJ7N2GBTSM7GQNANCNFSM4SRMKEBQ>.

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mwykes · 2020-11-12T09:03:10Z

Hi @Sham397243,
It looks like virtualenv is not installed. Could you run the commands you previously ran on 32-bit ubuntu to install virtualenv in your new 64-bit Ubuntu installation before running make install again?

cd katuali
sudo apt install python3-venv python3-pip
python3 -m pip install –user virtualenv
make install

Sham397243 · 2020-11-13T02:02:06Z

Hi mwykes, I could install virtualenv without using the term ‘-user’, but still having trouble with ‘make install’. Please see below. shamila@shamila-VirtualBox:~$ ls Desktop Downloads katuali Pictures Templates Documents examples.desktop Music Public Videos shamila@shamila-VirtualBox:~$ cd katuali shamila@shamila-VirtualBox:~/katuali$ python3 -m pip install –user virtualenv Invalid requirement: '–user' Traceback (most recent call last): File "/usr/share/python-wheels/packaging-16.6-py2.py3-none-any.whl/packaging/requirements.py", line 90, in __init__ req = REQUIREMENT.parseString(requirement_string) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 1125, in parseString raise exc File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 1115, in parseString loc, tokens = self._parse( instring, 0 ) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 989, in _parseNoCache loc,tokens = self.parseImpl( instring, preloc, doActions ) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 2378, in parseImpl loc, exprtokens = e._parse( instring, loc, doActions ) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 989, in _parseNoCache loc,tokens = self.parseImpl( instring, preloc, doActions ) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 2624, in parseImpl return self.expr._parse( instring, loc, doActions, callPreParse=False ) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 989, in _parseNoCache loc,tokens = self.parseImpl( instring, preloc, doActions ) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 2361, in parseImpl loc, resultlist = self.exprs[0]._parse( instring, loc, doActions, callPreParse=False ) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 993, in _parseNoCache loc,tokens = self.parseImpl( instring, preloc, doActions ) File "/usr/share/python-wheels/pyparsing-2.0.3-py2.py3-none-any.whl/pyparsing.py", line 1753, in parseImpl raise ParseException(instring, loc, self.errmsg, self) pyparsing.ParseException: Expected W:(abcd...) (at char 0), (line:1, col:1) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/pip/req/req_install.py", line 78, in __init__ req = Requirement(req) File "/usr/share/python-wheels/packaging-16.6-py2.py3-none-any.whl/packaging/requirements.py", line 94, in __init__ requirement_string[e.loc:e.loc + 8])) pip._vendor.packaging.requirements.InvalidRequirement: Invalid requirement, parse error at "'–user'" You are using pip version 8.1.1, however version 20.2.4 is available. You should consider upgrading via the 'pip install --upgrade pip' command. shamila@shamila-VirtualBox:~/katuali$ python3 -m pip install virtualenv Collecting virtualenv Downloading https://files.pythonhosted.org/packages/97/f3/c064343ac58d1a54c393a3f66483a29500f644a5918deeb935d28673edd9/virtualenv-20.1.0-py2.py3-none-any.whl (4.9MB) 100% |████████████████████████████████| 4.9MB 295kB/s Collecting appdirs<2,>=1.4.3 (from virtualenv) Downloading https://files.pythonhosted.org/packages/3b/00/2344469e2084fb287c2e0b57b72910309874c3245463acd6cf5e3db69324/appdirs-1.4.4-py2.py3-none-any.whl Collecting six<2,>=1.9.0 (from virtualenv) Downloading https://files.pythonhosted.org/packages/ee/ff/48bde5c0f013094d729fe4b0316ba2a24774b3ff1c52d924a8a4cb04078a/six-1.15.0-py2.py3-none-any.whl Collecting distlib<1,>=0.3.1 (from virtualenv) Downloading https://files.pythonhosted.org/packages/f5/0a/490fa011d699bb5a5f3a0cf57de82237f52a6db9d40f33c53b2736c9a1f9/distlib-0.3.1-py2.py3-none-any.whl (335kB) 100% |████████████████████████████████| 337kB 2.1MB/s Collecting importlib-resources>=1.0; python_version < "3.7" (from virtualenv) Downloading https://files.pythonhosted.org/packages/c5/1f/ec86d2a5c48ac6490d4471b297885603cf0e8da89d5ffbf0bce6e57f4d64/importlib_resources-3.3.0-py2.py3-none-any.whl Collecting filelock<4,>=3.0.0 (from virtualenv) Downloading https://files.pythonhosted.org/packages/93/83/71a2ee6158bb9f39a90c0dea1637f81d5eef866e188e1971a1b1ab01a35a/filelock-3.0.12-py3-none-any.whl Collecting importlib-metadata<3,>=0.12; python_version < "3.8" (from virtualenv) Downloading https://files.pythonhosted.org/packages/6d/6d/f4bb28424bc677bce1210bc19f69a43efe823e294325606ead595211f93e/importlib_metadata-2.0.0-py2.py3-none-any.whl Collecting zipp>=0.4; python_version < "3.8" (from importlib-resources>=1.0; python_version < "3.7"->virtualenv) Downloading https://files.pythonhosted.org/packages/41/ad/6a4f1a124b325618a7fb758b885b68ff7b058eec47d9220a12ab38d90b1f/zipp-3.4.0-py3-none-any.whl Installing collected packages: appdirs, six, distlib, zipp, importlib-resources, filelock, importlib-metadata, virtualenv Successfully installed appdirs distlib filelock importlib-metadata importlib-resources six-1.10.0 virtualenv zipp You are using pip version 8.1.1, however version 20.2.4 is available. You should consider upgrading via the 'pip install --upgrade pip' command. shamila@shamila-VirtualBox:~/katuali$ make install test -d venv || virtualenv venv --prompt '(katuali) ' --python=python3 AttributeError: module 'os' has no attribute 'PathLike' Makefile:16: recipe for target 'venv/bin/activate' failed make: *** [venv/bin/activate] Error 1 shamila@shamila-VirtualBox:~/katuali$ source venv/bin/activate bash: venv/bin/activate: No such file or directory shamila@shamila-VirtualBox:~/katuali$ From: mwykes <notifications@github.com> Sent: Thursday, 12 November 2020 8:03 PM To: nanoporetech/katuali <katuali@noreply.github.com> Cc: Abeynayake, Shamila <Shamila.Abeynayake@agriculture.gov.au>; Mention <mention@noreply.github.com> Subject: Re: [nanoporetech/katuali] Problem with installing Katuali (#13) [Marketing Mail] [SEC=UNCLASSIFIED] Hi @Sham397243<https://github.com/Sham397243>, It looks like virtualenv is not installed. Could you run the commands you previously ran on 32-bit ubuntu to install virtualenv in your new 64-bit Ubuntu installation before running make install again? cd katuali sudo apt install python3-venv python3-pip python3 -m pip install –user virtualenv make install — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#13 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARMFW7EJOZMHHLW7YBK5QG3SPOQF5ANCNFSM4SRMKEBQ>.

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mwykes · 2021-01-11T18:02:37Z

Hi @Sham397243,
Apologies for the slow reply. It looks like there have been some issues recently with virtualenv. Though the github virtualenv issue suggested that this was specific to python3.4, a stackoverflow post suggested people have also had the same issue with python3.5. Can you confirm which version of python you are using and also try again (there have been 4 minor releases of virtualenv since you encounted the problem, so it may well be fixed now).

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Problem with installing Katuali #13

Problem with installing Katuali #13

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Sham397243 commented Oct 28, 2020

pysam: no cython available - using pre-compiled C

pysam: htslib mode is shared

pysam: HTSLIB_CONFIGURE_OPTIONS=None

pysam: htslib configure options: None

mwykes commented Oct 28, 2020

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