Space Ranger1.1, printed on 11/13/2024
Space Ranger is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its required software dependencies, which are pre-compiled to run on a wide range of Linux distributions.
For convenience, the reference data package required for Space Ranger is provided as a separate download.
Step 1 – Download and unpack the Space Ranger file in any location. This example uses /opt.
$ cd /opt [ download file from downloads page ] $ tar -xzvf spaceranger-1.1.0.tar.gz
This unpacks Space Ranger, its dependencies, and the spaceranger script into a new directory called spaceranger-1.1.0.
Step 2 – Download and unpack any of the reference data files in a convenient location:
[ download file from downloads page ] $ tar -xzvf refdata-gex-GRCh38-2020-A.tar.gz
This creates a new directory called refdata-gex-GRCh38-2020-A that contains a single reference (in this case, GRCh38). Each reference contains a set of pre-generated indices and other data required by Space Ranger.
Step 3 – Prepend the Space Ranger directory to your $PATH. This allows you to invoke the spaceranger command.
If you unpacked both Space Ranger and the reference data into /opt, then run the following command:
$ export PATH=/opt/spaceranger-1.1.0:$PATH
For convenience, add this command to your .bashrc
Next, run the bundled site check script and send the output to 10x. If requested, we will review the information to ensure that Space Ranger runs smoothly once you have generated your own Visium data. Assuming you have installed Space Ranger as described above, run the following commands:
$ spaceranger sitecheck > sitecheck.txt $ spaceranger upload [email protected] sitecheck.txt
If you plan to run Space Ranger on a cluster, run and send us the output twice, once on a submit host and once on a cluster node.
If your system does not have direct Internet connectivity, send the output files as attachments to [email protected].
To ensure that the spaceranger pipeline is installed correctly, use spaceranger testrun. This test can take up to 60 minutes on a sixteen-core workstation. Assuming you have installed Space Ranger into /opt, the command to run the test looks like:
$ export PATH=/opt/spaceranger-1.1.0:$PATH $ spaceranger testrun --id=tiny spaceranger testrun 1.1.0 Copyright (c) 2016 10x Genomics, Inc. All rights reserved. ----------------------------------------------------------------------------- Martian Runtime - 4.0.0 Running preflight checks (please wait)... Checking sample info... Checking FASTQ folder... Checking reference... Checking reference_path (/opt/spaceranger-1.0.0/bin/../external/spaceranger_tiny_ref/1.0.0) Checking chemistry... Checking optional arguments... mrc: v3.2.5 mrp: v3.2.5 Anaconda: Python 2.7.15 :: Anaconda, Inc. numpy: 1.14.2 scipy: 1.0.1 pysam: 0.14.1 h5py: 2.8.0 pandas: 0.22.0 STAR: STAR_2.5.1b samtools: samtools 1.7 Using htslib 1.7 Copyright (C) 2018 Genome Research Ltd. 2019-11-21 14:36:29 [runtime] (ready) ID.tiny.SPATIAL_RNA_COUNTER_CS.SPATIAL_RNA_COUNTER.SPATIAL_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION 2019-11-21 14:36:29 [runtime] (run:local) ID.tiny.SPATIAL_RNA_COUNTER_CS.SPATIAL_RNA_COUNTER.SPATIAL_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION.fork0.chnk0.main 2019-11-21 14:36:29 [runtime] (ready) ID.tiny.SPATIAL_RNA_COUNTER_CS.SPATIAL_IMAGING_CS.STANDARDIZE_IMAGES 2019-11-21 14:36:29 [runtime] (run:local) ID.tiny.SPATIAL_RNA_COUNTER_CS.SPATIAL_IMAGING_CS.STANDARDIZE_IMAGES.fork0.split 2019-11-21 14:36:29 [runtime] (ready) ID.tiny.SPATIAL_RNA_COUNTER_CS.SPATIAL_RNA_COUNTER_PREP.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY ... Pipestance completed successfully!
|
If the server cannot access the Internet, you see an error that starts with:
[error] Could not retrieve spot layout data: To work around this, add the --unknown-slide argument to the testrun command line like this: spaceranger testrun --unknown-slide. If you plan to run the spaceranger count pipeline in an environment without access to the Internet, download the spot layout data for your slide from this link and provide this file to the spaceranger count pipeline using the --slidefile option, for example: spaceranger count --slidefile V02J31-001.json |
Whether the test pipestance succeeds or fails, you will see:
Saving diagnostics to tiny/tiny.mri.tgz
This tiny.mri.tgz file contains diagnostic information 10x can use to help resolve any problems. It is generated whether the pipeline succeeds or fails. If the pipeline fails and you need troubleshooting assistance, you can send this file directly to us from the command line:
$ spaceranger upload [email protected] tiny/tiny.mri.tgz
If your system does not have direct Internet connectivity, you can also send the file as an attachment to [email protected].