User: valdirbarth

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valdirbarth60
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Posts by valdirbarth

<prev • 10 results • page 1 of 1 • next >
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Comment: C: biopython not installed?
... you need to find the xml file of each tool (eg. get_codon_frequency.xml, it is inside the shed_tools folder somewhere). If you open that xml file, at the top you'll see the requirements for that tool inside tags. All you need to do is add biopython package as a requirement so it also installs it as ...
written 3 months ago by valdirbarth60
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Answer: A: Scipy error - no Fortran compiler found
... thank you!! For anyone who has the same issue, i downloaded and installed from here: https://gcc.gnu.org/wiki/GFortranBinaries ...
written 5 months ago by valdirbarth60
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Answer: A: Getting FTP uploaded files into the history of a local Galaxy
... hi joe, I suppose you are running Galaxy on a server that is not yours, correct? If so, the admin of the server is the one who is supposed to open the galaxy.ini (in the galaxy/config folder) file in the server and edit it to allow FTP uploads. If you do not have access to the file system of the se ...
written 5 months ago by valdirbarth60
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Scipy error - no Fortran compiler found
... I tried installing the scipy package which is required by some tool I need to run, but I get the **error: library dfftpack has Fortran sources but no Fortran compiler found** Any ideas how to solve this? Thank you! ...
scipy fortran written 5 months ago by valdirbarth60
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Answer: A: biopython not installed?
... Ok, I managed to get through this error by adding it as a requirement as a "package" instead of "python module" in the dependency XML file of the tool and installing the biopython package. thx ...
written 5 months ago by valdirbarth60
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6 follow
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biopython not installed?
... hi, I am using Ribo Tools in a local instance installed from the tool_shed (https://toolshed.g2.bx.psu.edu/repository?repository_id=f81548109cd9dd88). When i run it on my sample, it gives me the error: "line 16, in from Bio import SeqIO ImportError: No module named Bio" Which I googled and it ...
ribotools biopython written 5 months ago by valdirbarth60 • updated 3 months ago by taxicar00290
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Comment: A: not renaming dataset in workflow for Trim galore
... I still have not figured this out, anyone? ...
written 8 months ago by valdirbarth60
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Workflow renaming problem for tool with multiple outputs (Galaxy version 17.09) - Fix implemented at usegalaxy.org
... I have been successfully renaming outputs in my workflow. However I am having trouble renaming the outputs from Trim galore. I am using the usegalaxy.org server In the workflow section: > Rename dataset >This action will rename the output dataset. Click here > for more information. Vali ...
rename dataset galaxy workflow written 8 months ago by valdirbarth60 • updated 8 months ago by Jennifer Hillman Jackson25k
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Galaxy not PERMANENTLY deleting
... Hi, I just installed a new (Latest) galaxy in my Macbook and I realized that it is not permanently deleting the files from my hard drive (even though it says it was deleted, or even when I purge a whole history, the size of my galaxy folder stays the same when it should be 120 GB less). I had to man ...
deleting galaxy error written 8 months ago by valdirbarth60
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use bowtie for illumina with phred33?
... Hi, I am a newbie on this field. I am using usegalaxy.org tools, and bowtie for aligning sequences and for some reason the default that it uses is phred64 instead of phred33 (like the latest downloadable version of bowtie). The illumina seq files I get are phred33 and work perfectly in my local bowt ...
bowtie alignment rna-seq written 19 months ago by valdirbarth60 • updated 19 months ago by Jennifer Hillman Jackson25k

Latest awards to valdirbarth

Scholar 5 months ago, created an answer that has been accepted. For A: Getting FTP uploaded files into the history of a local Galaxy
Scholar 5 months ago, created an answer that has been accepted. For A: Scipy error - no Fortran compiler found

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