galaxy-upload 1.0.1

Installation

$ pip install galaxy-upload

$ python3 -m venv ~/galaxy-upload
$ . ~/galaxy-upload/bin/activate
$ pip install galaxy-upload

$ conda create -n galaxy-upload -c conda-forge -c bioconda galaxy-upload
$ conda activate galaxy-upload

$ docker run -it --rm -v "$(pwd):$(pwd)" -w "$(pwd)" -u "$(id -u):$(id -g)" \
    quay.io/biocontainers/galaxy-upload:1.0.0--pyhdfd78af_0 /bin/bash

$ docker run --rm -v "$(pwd):$(pwd)" -w "$(pwd)" -u "$(id -u):$(id -g)" \
    quay.io/biocontainers/galaxy-upload:1.0.0--pyhdfd78af_0 galaxy-upload

$ singularity run https://depot.galaxyproject.org/singularity/galaxy-upload:1.0.0--pyhdfd78af_0

$ singularity run https://depot.galaxyproject.org/singularity/galaxy-upload:1.0.0--pyhdfd78af_0 galaxy-upload

Usage

Upload a pair of fastq.gz files:

$ galaxy-upload --url https://usegalaxy.org \
    --api-key 70ffeec0ffeea11e1eaccede1337loaf --history-name 'Run 2' \
    RUN2_F_001.fastq.gz RUN2_R_001.fastq.gz
RUN2_F_001.fastq.gz ━━━━━━━━━━━━━━━━━━━━━━━━━━ 100/100 mB ? eta 0:00:00
RUN2_R_001.fastq.gz ━━━━━━━━━━━━━━━━━━━━━━━━━━ 100/100 mB ? eta 0:00:00

Required arguments are the Galaxy server URL and API key, and a history ID or name. Your API key can be found in the Galaxy UI after logging in, by navigating to User ⮕ Preferences ⮕ Manage API Key.

You can set the URL and API key options as environment variables to avoid retyping and prevent the key from being visible to other users in ps(1) output:

$ export GALAXY_URL=https://usegalaxy.org
$ export GALAXY_API_KEY=70ffeec0ffeea11e1eaccede1337loaf
$ galaxy-upload --history-name stuff reads.bam

When selecting a history by name, regular expression matching is used. If the name matches multiple histories, galaxy-upload will exit will output details about the matched histories and then exit with an error. You can then select the correct history ID using the --history-id option:

$ galaxy-upload --history-name stuff reads.bam
                          Active Histories
┏━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ID               ┃ Name        ┃ Last Modified            ┃
┡━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ 70ffeec0ffeead07 │ Newer stuff │ Mon Jul 11 15:54:05 2022 │
│ a11e1eaccedeble8 │ Older stuff │ Wed May 25 18:03:46 2022 │
└──────────────────┴─────────────┴──────────────────────────┘
ERROR: Multiple histories matching stuff found! Use --history-id to select one.
$ galaxy-upload --history-id 70ffeec0ffeead07 reads.bam
reads.bam ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 gB ? eta 0:00:00

If you want to find the correct history without attempting an upload, use the galaxy-history-search command. The --ignore-case option can be used to perform a case-insensitive search:

$ galaxy-history-search --ignore-case trinity
                           Active Histories
┏━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ID               ┃ Name                  ┃ Last Modified            ┃
┡━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ 084649feb42d4295 │ : test trinity inputs │ Wed Dec  9 10:02:35 2020 │
│ f697f94ca47080cf │ automate_trinity      │ Mon Dec 21 17:40:24 2015 │
│ c79278c7a37e619e │ TrinityRun            │ Fri Mar 10 14:21:56 2017 │
│ ee31286b26ff3352 │ trinity               │ Wed Sep 30 09:04:03 2020 │
└──────────────────┴───────────────────────┴──────────────────────────┘

Regular expressions are supported, for example, to find only the histories with names ending with trinity:

$ galaxy-history-search --ignore-case 'trinity$'
                         Active Histories
┏━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ID               ┃ Name             ┃ Last Modified            ┃
┡━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ f697f94ca47080cf │ automate_trinity │ Mon Dec 21 17:40:24 2015 │
│ ee31286b26ff3352 │ trinity          │ Wed Sep 30 09:04:03 2020 │
└──────────────────┴──────────────────┴──────────────────────────┘

Multiple options mirror those of the Galaxy UI’s upload dialog, including --file-type, --dbkey, and --space-to-tab. The --file-name option can be used when uploading single files to control the file name in the history (by default it will be the same as the name on the local filesystem).

To support resuming interrupted uploads, use the --storage option to point to a state file (it will be created if it does not exist):

$ galaxy-upload --file-type bam --file-name Reads --storage /data/upload.txt /data/reads.bam

If the upload is interrupted, simply repeat the same command to resume uploading from the point of interruption.

Note that if you are trying to re-upload (not resume) a file that you have already uploaded once before, you will need to remove it from the storage file or use a different storage file.

1.0.1

• Document installation/usage with conda and containers by @natefoo in https://github.com/galaxyproject/galaxy-upload/pull/7

• Use click to require file arg to exist by @natefoo in https://github.com/galaxyproject/galaxy-upload/pull/9

• Pin tuspy to !=1.0.1 due to issue with upload_chunk(). by @natefoo in https://github.com/galaxyproject/galaxy-upload/pull/10

1.0.0

• Initial release

0.0.1

• Initial prerelease for comment and testing