Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[SYNPY-1522] Add note on lost shared libraries to install instructions for conda #1140

Merged
merged 1 commit into from
Oct 4, 2024
Merged

[SYNPY-1522] Add note on lost shared libraries to install instructions for conda #1140

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 21 additions & 2 deletions docs/tutorials/installation.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,18 @@

By following the instructions below, you are installing the `synapseclient`, `synapseutils` and the command line client.

## PyPI
## TL;DR For Experts
1. Set up your Python development environment in your preferred manner (e.g. with `conda`, `pyenv`, etc).
2. Run
```
pip install --upgrade synapseclient
```
3. Verify your installation
```
pip show synapseclient
```

## Installation Guide For: PyPI Users

The [synapseclient](https://pypi.python.org/pypi/synapseclient/) package is available from PyPI. It can be installed or upgraded with pip. Due to the nature of Python, we highly recommend you set up your python environment with [conda](https://www.anaconda.com/products/distribution) or [pyenv](https://github.com/pyenv/pyenv) and create virtual environments to control your Python dependencies for your work.

Expand All @@ -20,6 +31,14 @@ pip install --upgrade "synapseclient[pandas]"
pip install --upgrade "synapseclient[pandas, pysftp, boto3]"
```

> **NOTE** <br>
> The `synapseclient` package may require loading shared libraries located in your system's `/usr/local/lib` directory. Some users working
with `conda` have experienced issues with shared libraries not being found due to the system searching in the wrong locations. Although
not recommended, one solution for this is manually configuring the `LD_LIBRARY_PATH` environment variable to point
to the `/usr/local/lib` directory. [See here](https://github.com/conda/conda/issues/12800) for more context on this solution, and for alternatives.
jaymedina marked this conversation as resolved.
Show resolved Hide resolved

----

- pyenv: Use [virtualenv](https://virtualenv.pypa.io/en/latest/) to manage your python environment:

```bash
Expand All @@ -42,7 +61,7 @@ python3 -m pip3 install --upgrade "synapseclient[pandas, pysftp, boto3]"

The dependencies on pandas, pysftp, and boto3 are optional. The Synapse `synapseclient.table` feature integrates with Pandas. Support for sftp is required for users of SFTP file storage. Both require native libraries to be compiled or installed separately from prebuilt binaries.

## Local
## Installation Guide For: Git Users

Source code and development versions are [available on Github](https://github.com/Sage-Bionetworks/synapsePythonClient). Installing from source:

Expand Down
Loading