install issues

[rohan-bareja-turnstone]

hello,

Both pip and conda install show different usages as compared to shown on the readme.
Conda install : https://anaconda.org/bioconda/rna-seqc

usage from conda install:

~/anaconda3/bin/rna-seqc
RNA-SeQC v1.1.8.1 07/11/14
Missing required options: s, t, r, o
usage: java -jar RNA-SeQC.jar
-bwa Path to BWA, which should be set if it's not
in your path and BWArRNA is used.
-BWArRNA Use an on the fly BWA alignment for estimating
rRNA content. The value should be the rRNA
reference fasta.
-corr GCT file for expression correlation comparison
-d Perform downsampling to the given number of
reads.
-e Change the definition of a transcripts end (5'
or 3') to the given length. (10,
50, 100 are acceptable values)
-expr Uses provided GCT file for expression values
instead of on-the-fly RPKM calculation
-gatkFlags A string of flags that will be passed on to
the GATK
-gc File of transcript id gc content. Used
for stratification.
-gcMargin Used in conjunction with '-strat gc' to
specify the percent gc content to use as
boundaries. E.g. .25 would set a lower cutoff
of 25% and an upper cutoff of 75%.
-gld Gap Length Distribution: plots the
distribution of gap length.
-n Number of top transcripts to use.
-noDoC Suppresses GATK Depth of Coverage
calculations.
-noReadCounting Suppresses read count-based metrics.
-o Output directory (will be created if doesn't
exist).
-r Reference Genome in fasta format.
-rRNA intervalFIle for rRNA loci (must end in .list)
-rRNAdSampleTarget Downsamples to calculate rRNA rate more
efficiently. Default is 1 million. Set to 0 to

Pip install : pip install rnaseqc

usage from pip install

python3 -m rnaseqc -h
usage: rnaseqc [-h] {run,aggregate,notebook,report,insert-size,legacy-exons} ...

positional arguments:
{run,aggregate,notebook,report,insert-size,legacy-exons}
run A light wrapper with some convenience functions to run RNA-SeQC
aggregate Aggregate RNA-SeQC outputs from multiple samples
notebook Generate a notebook with figures comparing outputs from multiple samples
report Generate PDF figures from aggregated RNA-SeQC results
insert-size Generate a BED file with long (>1000bp), high-mappability intervals for estimating insert
sizes
legacy-exons Renames exons in exon_reads.gct file from RNA-SeQC 2 to use naming convention from RNA-SeQC
1.1.x

optional arguments:
-h, --help show this help message and exit

Whats the best way to install this package?

Thanks
Rohan

[agraubert]

The anaconda package is a legacy version of RNA-SeQC maintained by another group.
The pip package rnaseqc, is a support module for aggregating data from RNA-SeQC.
The best way to install the RNA-SeQC program is to download one of the gzipped static executables from our releases page or to use our docker image gcr.io/broad-cga-aarong-gtex/rnaseqc

[pblumenkamp]

Sorry to reply to such an old issue. Would it be possible to bring RNA-SeQC 2 to bioconda? Maybe as anew package called 'rna-seqc2' if it should not be mixed up with the existing conda package.

Thanks,
Patrick