Document for install BALSAMIC from source code

[yiyi1247]

Hi I have been following this guide to install BALSAMIC ; however the linux machine/environment I am utilizing has no internet access. so I could not follow straight up the installation guide from before. I cannot use conda and nor could i use pip.

However, I could upload tar ball or zipped file to this linux environment. I can upload the source code to this environment. I wonder what should I do next to be able too get the balsamic command and pipeline running. I could not find any guide on this. Could someone please help me? Thanks in advance!

Right now I could only upload the source code...The environmenthas python and everything preinstalled and if there is additional dependency I could upload too. But I do need some guidance here.

$ bash run_validate.sh
analysis dir set to  run_tests/
+ balsamic --loglevel INFO config case -w balsamic -t tests/test_data/fastq/S1_R_1.fastq.gz --case-id _ --analysis-dir run_tests/ --balsamic-cache /home/proj/stage/cancer/balsamic_cache
run_validate.sh: line 104: balsamic: command not found

[ivadym]

Hello, thanks for your interest!

I would recommend that you try installing it first on your local machine and become familiar with the CLI. Once you successfully install it, along with all the reference files needed for analysis, you can follow these steps:

1. Download BALSAMIC source code and upload it to your offline Linux environment
2. Make sure that all required dependencies for BALSAMIC are installed on your machine.
3. Install BALSAMIC. Since you cannot use Conda or Pip, you'll need to build BALSAMIC from the source code manually.
4. Download BALSAMIC reference cache. You can try to download it on a machine with internet access and then transfer it to your offline Linux environment and place it in a directory where you can access it during analysis. (https://balsamic.readthedocs.io/en/latest/install.html#step-2-generate-balsamic-cache-and-pull-containers).
5. Now that you have installed BALSAMIC and have the reference cache ready, you can run BALSAMIC commands as needed (https://balsamic.readthedocs.io/en/latest/user_guide.html). Make sure to provide the correct paths to the balsamic cache and other input files.

Note also that you'll need a COSMIC authorization and a valid Sentieon license to run the analysis.

[yiyi1247]

Great, thank you! @ivadym for the very detailed explanation, silly me, how do we build the BALSAMIC from the source code manually? Could you please enlighten me a bit at step 3. I think I am clear with the rest of steps! Thanks in advance

[yiyi1247]

I somehow found this, not sure if it is correct way: I could build wheel by running python setup.py sdist bdist_wheel and then i could run pip install BALSAMIC-12.0.2-py3-none-any.whl

but getting many errors

[leile@sens2023551-bianca dist]$ pip install BALSAMIC-12.0.2-py3-none-any.whl
Processing ./BALSAMIC-12.0.2-py3-none-any.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e83c8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e8cc0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e8588>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e8780>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e8dd8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
ERROR: Could not find a version that satisfies the requirement pydantic<2.0,>=1.9.0 (from BALSAMIC==12.0.2) (from versions: none)
ERROR: No matching distribution found for pydantic<2.0,>=1.9.0 (from BALSAMIC==12.0.2)

[yiyi1247]

I feel I am doing it wrong, I install BALSAMIC's wheel and then I need to install its dependency wheel, and then I install dependency 'dependency wheel, and then next dependency of dependency 'dependency wheel...

Requirement already satisfied: wheel in /sw/comp/python/3.7.2_rackham/lib/python3.7/site-packages (0.33.1)
Processing ./dist/BALSAMIC-12.0.2-py3-none-any.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b580115b8d0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/gsutil/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b580115ba58>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/gsutil/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b580115b278>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/gsutil/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b580115beb8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/gsutil/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b580115bfd0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/gsutil/
ERROR: Could not find a version that satisfies the requirement gsutil==5.23 (from BALSAMIC==12.0.2) (from versions: none)
ERROR: No matching distribution found for gsutil==5.23 (from BALSAMIC==12.0.2)
[leile@sens2023551-bianca BALSAMIC]$ ls
assets             build          codecov.yml  config      container_tests  __init__.py  README.rst            run_validate.sh  tests           workflows
BALSAMIC           CHANGELOG.rst  commands     constants   dist             LICENSE      requirements-dev.txt  setup.py         utils
BALSAMIC.egg-info  CITATION.cff   conda        containers  docs             MANIFEST.in  run_tests             snakemake_rules  __version__.py
[leile@sens2023551-bianca BALSAMIC]$ cd build/
[leile@sens2023551-bianca build]$ ls
bdist.linux-x86_64  lib
[leile@sens2023551-bianca build]$ bdist.linux-x86_64/
-bash: bdist.linux-x86_64/: Is a directory
[leile@sens2023551-bianca build]$ cd bdist.linux-x86_64/
[leile@sens2023551-bianca bdist.linux-x86_64]$ ls
[leile@sens2023551-bianca bdist.linux-x86_64]$ ls
[leile@sens2023551-bianca bdist.linux-x86_64]$ ls -a
.  ..
[leile@sens2023551-bianca bdist.linux-x86_64]$ cd ..
[leile@sens2023551-bianca build]$ ls
bdist.linux-x86_64  lib
[leile@sens2023551-bianca build]$ cd lib/
[leile@sens2023551-bianca lib]$ ls
assets  BALSAMIC  commands  config  constants  containers  snakemake_rules  tests  utils  workflows
[leile@sens2023551-bianca lib]$ cd BALSAMIC/
[leile@sens2023551-bianca BALSAMIC]$ ls
assets  commands  config  constants  containers  __init__.py  snakemake_rules  utils  __version__.py  workflows
[leile@sens2023551-bianca BALSAMIC]$ cd ..
[leile@sens2023551-bianca lib]$ cd ..
[leile@sens2023551-bianca build]$ cd ..
[leile@sens2023551-bianca BALSAMIC]$ pip --version
pip 19.3.1 from /sw/comp/python/3.7.2_rackham/lib/python3.7/site-packages/pip (python 3.7)
[leile@sens2023551-bianca BALSAMIC]$ pip install .
Processing /castor/project/proj/wgs_nes/BALSAMIC
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b2685cc40b8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/click/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b2685cc43c8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/click/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b2685d1ad30>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/click/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b2685d1d198>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/click/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b2685d1def0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/click/
ERROR: Could not find a version that satisfies the requirement click==8.1.3 (from BALSAMIC==12.0.2) (from versions: none)
ERROR: No matching distribution found for click==8.1.3 (from BALSAMIC==12.0.2)
[leile@sens2023551-bianca BALSAMIC]$ ls
assets             build          codecov.yml  config      container_tests  __init__.py  README.rst            run_validate.sh  tests           workflows
BALSAMIC           CHANGELOG.rst  commands     constants   dist             LICENSE      requirements-dev.txt  setup.py         utils
BALSAMIC.egg-info  CITATION.cff   conda        containers  docs             MANIFEST.in  run_tests             snakemake_rules  __version__.py
[leile@sens2023551-bianca BALSAMIC]$ cd dist/
[leile@sens2023551-bianca dist]$ ls
BALSAMIC-12.0.2-py3-none-any.whl  BALSAMIC-12.0.2.tar.gz
[leile@sens2023551-bianca dist]$ pip install BALSAMIC-12.0.2-py3-none-any.whl
Processing ./BALSAMIC-12.0.2-py3-none-any.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b6ccdad8828>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/tabulate/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b6ccdad87b8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/tabulate/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b6ccdad82e8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/tabulate/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b6ccdad8470>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/tabulate/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b6ccda17a90>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/tabulate/
ERROR: Could not find a version that satisfies the requirement tabulate==0.8.10 (from BALSAMIC==12.0.2) (from versions: none)
ERROR: No matching distribution found for tabulate==0.8.10 (from BALSAMIC==12.0.2)
[leile@sens2023551-bianca dist]$ module spider pytest
Lmod has detected the following error:  Unable to find: "pytest".

[leile@sens2023551-bianca dist]$ module spider tabulate
Lmod has detected the following error:  Unable to find: "tabulate".

[leile@sens2023551-bianca dist]$ pip install BALSAMIC-12.0.2-py3-none-any.whl
Processing ./BALSAMIC-12.0.2-py3-none-any.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e83c8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e8cc0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e8588>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e8780>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2b0d051e8dd8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic/
ERROR: Could not find a version that satisfies the requirement pydantic<2.0,>=1.9.0 (from BALSAMIC==12.0.2) (from versions: none)
ERROR: No matching distribution found for pydantic<2.0,>=1.9.0 (from BALSAMIC==12.0.2)
[leile@sens2023551-bianca dist]$ module spider pydantic
Lmod has detected the following error:  Unable to find: "pydantic".

[leile@sens2023551-bianca dist]$ module spider pydantic 2.4.2
Lmod has detected the following error:  Unable to find: "pydantic".

[leile@sens2023551-bianca dist]$ module spider pydantic/2.4.2
Lmod has detected the following error:  Unable to find: "pydantic/2.4.2".

[leile@sens2023551-bianca dist]$ ls
BALSAMIC-12.0.2-py3-none-any.whl  BALSAMIC-12.0.2.tar.gz
[leile@sens2023551-bianca dist]$ cp -r /proj/sens2023551/nobackup/wharf/leile/leile-sens2023551/pydantic-2.4.2-py3-none-any.whl ./pydantic.whl
[leile@sens2023551-bianca dist]$ ls
BALSAMIC-12.0.2-py3-none-any.whl  BALSAMIC-12.0.2.tar.gz  pydantic.whl
[leile@sens2023551-bianca dist]$ pip install pydantic.whl
ERROR: pydantic.whl is not a valid wheel filename.
[leile@sens2023551-bianca dist]$ mv pydantic.whl /pydantic-2.4.2-py3-none-any.whl
mv: cannot create regular file ‘/pydantic-2.4.2-py3-none-any.whl’: Permission denied
[leile@sens2023551-bianca dist]$ mv pydantic.whl pydantic-2.4.2-py3-none-any.whl
[leile@sens2023551-bianca dist]$ ls
BALSAMIC-12.0.2-py3-none-any.whl  BALSAMIC-12.0.2.tar.gz  pydantic-2.4.2-py3-none-any.whl
[leile@sens2023551-bianca dist]$ pip install pydantic-2.4.2-py3-none-any.whl
Processing ./pydantic-2.4.2-py3-none-any.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ac623959cc0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic-core/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ac6239595c0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic-core/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ac623959518>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic-core/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ac623959438>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic-core/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ac623959358>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pydantic-core/
ERROR: Could not find a version that satisfies the requirement pydantic-core==2.10.1 (from pydantic==2.4.2) (from versions: none)
ERROR: No matching distribution found for pydantic-core==2.10.1 (from pydantic==2.4.2)
[leile@sens2023551-bianca dist]$ cp -r /proj/sens2023551/nobackup/wharf/leile/leile-sens2023551/pydantic-1.9.0-py3-none-any.whl ./pydantic-1.9.0-py3-none-any.whl
[leile@sens2023551-bianca dist]$ pip install pydantic-1.9.0-py3-none-any.whl
Processing ./pydantic-1.9.0-py3-none-any.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ab013dc7710>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/typing-extensions/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ab013dc7828>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/typing-extensions/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ab013dc74e0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/typing-extensions/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ab013dc7550>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/typing-extensions/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x2ab013dc76d8>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/typing-extensions/
ERROR: Could not find a version that satisfies the requirement typing-extensions>=3.7.4.3 (from pydantic==1.9.0) (from versions: none)
ERROR: No matching distribution found for typing-extensions>=3.7.4.3 (from pydantic==1.9.0)
[leile@sens2023551-bianca dist]$ cp -r /proj/sens2023551/nobackup/wharf/leile/leile-sens2023551/typing_extensions-4.8.0-py3-none-any.whl ./typing_extensions-4.8.0-py3-none-any.whl
[leile@sens2023551-bianca dist]$ ls
BALSAMIC-12.0.2-py3-none-any.whl  BALSAMIC-12.0.2.tar.gz  pydantic-1.9.0-py3-none-any.whl  pydantic-2.4.2-py3-none-any.whl  typing_extensions-4.8.0-py3-none-any.whl
[leile@sens2023551-bianca dist]$ pip install typing_extensions-4.8.0-py3-none-any.whl
Processing ./typing_extensions-4.8.0-py3-none-any.whl
ERROR: Package 'typing-extensions' requires a different Python: 3.7.2 not in '>=3.8'
[leile@sens2023551-bianca dist]$ module spider python

---------------------------------------------------------------------------------------------------------------------------------------------------------------------
  python:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------
     Versions:
        python/2.7.6
        python/2.7.9
        python/2.7.11
        python/2.7.15
        python/3.3
        python/3.3.1
        python/3.4.3
        python/3.5.0
        python/3.6.0
        python/3.6.8
        python/3.7.2
        python/3.8.7
        python/3.9.5
        python/3.10.8
        python/3.11.4
     Other possible modules matches:
        Biopython  Boost.Python  Python  biopython  flatbuffers-python  netcdf4-python  protobuf-python  python-parasail  python3  python_GIS_packages  python_ML_package
s  wrf-python

---------------------------------------------------------------------------------------------------------------------------------------------------------------------
  To find other possible module matches execute:

      $ module -r spider '.*python.*'

---------------------------------------------------------------------------------------------------------------------------------------------------------------------
  For detailed information about a specific "python" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:
[leile@sens2023551-bianca dist]$ module load python/3.8.7

The following have been reloaded with a version change:
  1) python/3.7.2 => python/3.8.7

[leile@sens2023551-bianca dist]$ pip install typing_extensions-4.8.0-py3-none-any.whl
Defaulting to user installation because normal site-packages is not writeable
Processing ./typing_extensions-4.8.0-py3-none-any.whl
Installing collected packages: typing-extensions
Successfully installed typing-extensions-4.8.0
[leile@sens2023551-bianca dist]$ pip install pydantic-1.9.0-py3-none-any.whl
Defaulting to user installation because normal site-packages is not writeable
Processing ./pydantic-1.9.0-py3-none-any.whl
Requirement already satisfied: typing-extensions>=3.7.4.3 in /castor/project/home/leile/.local/lib/python3.8/site-packages (from pydantic==1.9.0) (4.8.0)
Installing collected packages: pydantic
Successfully installed pydantic-1.9.0
[leile@sens2023551-bianca dist]$ pip install
BALSAMIC-12.0.2-py3-none-any.whl          pydantic-1.9.0-py3-none-any.whl           typing_extensions-4.8.0-py3-none-any.whl
BALSAMIC-12.0.2.tar.gz                    pydantic-2.4.2-py3-none-any.whl
[leile@sens2023551-bianca dist]$ pip install BALSAMIC-12.0.2-py3-none-any.whl
Defaulting to user installation because normal site-packages is not writeable
Processing ./BALSAMIC-12.0.2-py3-none-any.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2abd8e4052b0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/numpy/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2abd8e40d370>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/numpy/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2abd8e416160>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/numpy/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2abd8e416af0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/numpy/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2abd8e416940>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/numpy/
ERROR: Could not find a version that satisfies the requirement numpy>=1.21.6 (from balsamic)
ERROR: No matching distribution found for numpy>=1.21.6
[leile@sens2023551-bianca dist]$ pip install BALSAMIC-12.0.2-py3-none-any.whl
Defaulting to user installation because normal site-packages is not writeable
Processing ./BALSAMIC-12.0.2-py3-none-any.whl
Requirement already satisfied: toml==0.10.2 in /sw/comp/python/3.8.7_rackham/lib/python3.8/site-packages (from BALSAMIC==12.0.2) (0.10.2)
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b01afa0dbe0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/cyvcf2/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b01af9d9340>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/cyvcf2/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b01af9d9490>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/cyvcf2/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b01af9dcb20>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/cyvcf2/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b01af9ee3a0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/cyvcf2/
ERROR: Could not find a version that satisfies the requirement cyvcf2==0.30.22 (from balsamic)
ERROR: No matching distribution found for cyvcf2==0.30.22
[leile@sens2023551-bianca dist]$ pip install BALSAMIC-12.0.2-py3-none-any.whl ^C
[leile@sens2023551-bianca dist]$ pwd
/proj/sens2023551/wgs_nes/BALSAMIC/dist
[leile@sens2023551-bianca dist]$ cp -R /proj/sens2023551/nobackup/wharf/leile/leile-sens2023551/cyvcf2-0.30.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
 ./cyvcf2-0.30.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
[leile@sens2023551-bianca dist]$ pip install cyvcf2-0.30.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Defaulting to user installation because normal site-packages is not writeable
ERROR: cyvcf2-0.30.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl is not a supported wheel on this platform.
[leile@sens2023551-bianca dist]$ cp -R /proj/sens2023551/nobackup/wharf/leile/leile-sens2023551/cyvcf2-0.30.22-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl ./cyvcf2-0.30.22-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
[leile@sens2023551-bianca dist]$ pip install cyvcf2-0.30.22-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Defaulting to user installation because normal site-packages is not writeable
Processing ./cyvcf2-0.30.22-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b8bca609a30>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/coloredlogs/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b8bca609c40>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/coloredlogs/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b8bca609df0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/coloredlogs/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b8bca609fa0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/coloredlogs/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2b8bcb8e3190>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/coloredlogs/
ERROR: Could not find a version that satisfies the requirement coloredlogs (from cyvcf2)
ERROR: No matching distribution found for coloredlogs
[leile@sens2023551-bianca dist]$ cp -R /proj/sens2023551/nobackup/wharf/leile/leile-sens2023551/coloredlogs-15.0.1-py2.py3-none-any.whl ./coloredlogs-15.0.1-py2.py3-none-any.whl
[leile@sens2023551-bianca dist]$ pip install coloredlogs-15.0.1-py2.py3-none-any.whl
Defaulting to user installation because normal site-packages is not writeable
Processing ./coloredlogs-15.0.1-py2.py3-none-any.whl
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2ab6b4f88e20>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/humanfriendly/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2ab6b4f37fd0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/humanfriendly/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2ab6b4f374c0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/humanfriendly/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2ab6b4f92a30>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/humanfriendly/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x2ab6b4f921f0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/humanfriendly/
ERROR: Could not find a version that satisfies the requirement humanfriendly>=9.1 (from coloredlogs)
ERROR: No matching distribution found for humanfriendly>=9.1