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ICGC-TCGA-PanCancer / fastq-uploader

This tool is inteded to be used to upload fastq files for the PanCancer project
GNU General Public License v2.0
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Directory Issues #3

Closed kaboroevich closed 9 years ago

kaboroevich commented 9 years ago

I have a few issues regarding the directory paths generated in gnos_upload_fastq.pl

1) Is line 111 supposed to be $output_dir = "fastq/$output_dir" and not $output_dir = "$output_dir/fastq"? The former prevents running the code from a directory without write permissions.

2) Why is the file name prefixed with $pwd on line 125 my $command = "$link_method $pwd/$file $output_dir";? This causes a missing link to be created in the $output_dir.

Regards, Keith

kaboroevich commented 9 years ago

I've edit the file as follows and have made some progress: Commented out line 110 Removed $pwd from all lines.

I know get the error in the upload.log, Error: No such file or directory (errno = 2) FileName: 126d4534-e1c6-11e4-b007-84857beeaedb//share/icgc_pan/150406_PCAWG_RNAseq_upload_work, however, I cannot find where this strange directory combination comes from. My manifest.xml is as follows:

<?xml version="1.0" encoding="utf-8"?>
<SUBMISSION center_name="RIKEN" created_by="cgsubmit 3.1.1" submission_date="2015-04-13T10:15:58.422235" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="GeneTorrentManifest.xsd">
  <SERVER_INFO server_path="126d4534-e1c6-11e4-b007-84857beeaedb" submission_uri="https://gtrepo-riken.annailabs.com/cghub/data/analysis/upload/126d4534-e1c6-11e4-b007-84857beeaedb"/>
  <FILES>
    <FILE checksum="8d0a66b0ce03338f1b5af4a8ff41bdff" checksum_method="MD5" filename="/share/icgc_pan/150406_PCAWG_RNAseq_upload_work/icgc_rna_RNA_RK019_cancer_20120622_01.fastq.tar.gz" filetype="fasta"/>
  </FILES>
</SUBMISSION>

Does gtupload use / as the filepath? The linked files are in '126d4534-e1c6-11e4-b007-84857beeaedb'

kaboroevich commented 9 years ago

I've worked around the issue but executing the script in the directory containing the data files (fastq, meta, md5) and leaving in the references to $pwd.