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Hey there! I'm running Galaxy 18.05 on a server, I have a tool that creates some javascript html output which I have whitelisted. I still get
javascript is needed to display data.
If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
If I donwload the file it displays no problem.. I checked the whitelist config file and the tool that produced it is listed there. FastQC works fine.
qname_input_sorted.bam
and the subsequent tools will require that as input. However, it seems galaxy will not accept this format for upload(?) - i.e. i don't know how to write a test that has this param: <param name="mapping_output" value="mapped_reads.bam" ftype="qname_input_sorted.bam"/>
- the error message I get is: `An invalid option was selected for file_type qname_input_sorted please verify'
qnamed_sorted.bam
. qname_input_sorted.bam
is for aligners that were run in galaxy and that output the reads in the order that they were read in. This isn't the official "SO:queryname", but qname_sorted.bam
is compatible with qname_input_sorted.bam
, so there will be no additional conversion
rm
it and try again ?
---------------------- >> begin tool stdout << -----------------------
Deduplicating with: 'deduplicate_bismark -s submitted_reads.bam --bam'
Processing single-end Bismark output file(s) (SAM format):
submitted_reads.bam
If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.
Checking file >>submitted_reads.bam<< for signs of file truncation...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Output file is: submitted_reads.deduplicated.bam
Total number of alignments analysed in submitted_reads.bam: 554
Total number duplicated alignments removed: 50 (9.03%)
Duplicated alignments were found at: 44 different position(s)
Total count of deduplicated leftover sequences: 504 (90.97% of total)
skipping header line: @HD VN:1.0 SO:queryname
skipping header line: @SQ SN:chrY_JH584300_random LN:182347
skipping header line: @SQ SN:chrY_JH584301_random LN:259875
skipping header line: @SQ SN:chrY_JH584302_random LN:155838
skipping header line: @SQ SN:chrY_JH584303_random LN:158099
skipping header line: @PG ID:Bismark VN:v0.19.1 CL:"bismark --bam --gzip --temp_dir /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpn4m609_i -o /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpn4m609_i/results --quiet --fastq -L 20 -D 15 -R 2 --un --ambiguous /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpe8nkca8w /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpDiq_J8/files/000/dataset_2.dat"
----------------------- >> end tool stdout << ------------------------
---------------------- >> begin tool stderr << -----------------------
----------------------- >> end tool stderr << ------------------------
FAIL