Installation and Usage questions

[santiagorevale]

Hi Mathew,

I'm finally ready to give it a go to your pipeline. I have a few questions to ask you first, some regarding the installation and some other to the usage.

Re installation:

1. Is there a reason behind using Anaconda instead of it's minimal sibling Miniconda?

2. The standard make command did not work because of a path length issue with some conda packages. I couldn't sort it out, because I'm not able to have a shorter path where to compile ORP in (I'm working on a cluster and my initial path is already quite long). Even though I'm pursuing already a different solution, would it be possible to shrink the path from software/anaconda/install to simply software/conda? It doesn't sound like much, but it would have made the difference to me.

3. I tried creating the docker instance on my own, but I've got the following error:

...
cd /home/orp/Oyster_River_Protocol/software/anaconda && bash Anaconda3-2019.10-Linux-x86_64.sh -b -p install/
PREFIX=/home/orp/Oyster_River_Protocol/software/anaconda/install
Unpacking payload ...
Collecting package metadata (current_repodata.json): ...working... done                                              
Solving environment: ...working... done
...
Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
echo ". /home/orp/Oyster_River_Protocol/software/anaconda/install/etc/profile.d/conda.sh" >> ~/.bashrc;
source ~/.bashrc;
( \
			conda activate; \
			conda update -y -n base conda; \
			conda deactivate; \
 )
/bin/bash: line 1: conda: command not found
/bin/bash: line 2: conda: command not found
/bin/bash: line 3: conda: command not found
make: *** [orp] Error 127
Makefile:45: recipe for target 'orp' failed
The command '/bin/sh -c cd Oyster_River_Protocol && sudo make' returned a non-zero code: 2

I don't get why it's not working, the source command should be initialising conda, but it's not.

4. Again regarding creating the docker instance, I would like to make a few changes to it, but I'm not sure how. I would like to use the newer version of Trinity (2.9.0). Because it's not available through conda, I was looking into installing it through your Makefile file, like you are installing transabyss or OrthoFuser. However, I don't have experience in creating makefiles, so I'm not sure what should I be adding to it. Would you be able to help me with this?

5. When are you planning on releasing the next version? I've noticed you have already made some changes to conda and bumped Spades to version 3.14, which is another thing I was looking into it.

Re usage:

6. I would like to be able to provide to the pipeline some additional transcriptome assemblies to be incorporated into the assembly merging step (OrthoFuse). Is that possible? I seem to recall having read somewhere that OrthFuse was created in such a way it could take additional assemblies. If this is so, how can I do it? If ORP cannot be setup to run this way, would it be possible to run everything from OrthoFuser onwards providing the additional assemblies? Any other recommendation?

The reason why I would like to be able to do this is because I'm trying to build a comprehensive transcriptome for different fly species (independently), and I have several sets of RNAseq data from different tissues/states/individuals/generations/lines (depending on the specie). I also have a reference genome for some of them. So my idea based on some of your previous comments (on GitHub) would be to assemble each dataset individually, both de novo and reference guided, and then merge them as instructed in your pipeline (OrthoFurse, Transrate, Detonate, etc.). What do you think?

Thank you very much in advance for anything you could help me with.

Cheers,
Santiago

[santiagorevale]

Hi @macmanes , were you able to look into this? Any tips or advice?

Also, I've noticed that you've been doing some changes. Any ETA on the next release?

Thanks in advance.

Cheers,
Santiago