Initial install won't run - get errors about ImageMagick delegate?

[vin...@hkl.hms.harvard.edu]

Installed all dependencies (using BioGrids Installer), installed pigx-0.0.3 and pigx_rnaseq-0.0.5 from the release targz files.  All dependencies were found, no errors on installation.

Upon running either pigx binary or pigx_rnaseq binary I find a stray ^L in the source just before the first import statement:

# You should have received a copy of the GNU General Public License

# along with this program.  If not, see <http://www.gnu.org/licenses/>.

^L

import os

import sys

import argparse

import shutil

and again after args parsing:

 76 args = parser.parse_args()

 77 

 78 ^L

and of course this produces an error when run:

./pigx: line 30: ^L: command not found

After removing the two ^L and running again I get error messages about X11 delegate:

 import: delegate library support not built-in '' (X11) @ error/import.c/ImportImageCommand/1297.

  2 Version: ImageMagick 7.0.7-22 Q16 x86_64 2018-01-22 http://www.imagemagick.org

  3 Copyright: © 1999-2018 ImageMagick Studio LLC

  4 License: http://www.imagemagick.org/script/license.php

  5 Features: Cipher DPC HDRI Modules

  6 Delegates (built-in): bzlib freetype jng jpeg ltdl lzma png tiff xml zlib

  7 Usage: import [options ...] [ file ]

  8 

The delegate error message is repeated four times. 

Any idea what's going on here? Not sure where Imagemagick errors are coming from. 

Jim

[Ricardo Wurmus]

Hi,

> Installed all dependencies (using BioGrids Installer), installed pigx-0.0.3
> and pigx_rnaseq-0.0.5 from the release targz files. All dependencies were
> found, no errors on installation.

How did you install from the archives? (Just so we know nothing went
wrong there.)

> Upon running either pigx binary or pigx_rnaseq binary I find a stray ^L in
> the source just before the first import statement:

The ^L is a page break character. Editors can display this as a line,
for example. It has no effect on executing the script as it’s merely a
control character such as a line break (^M).

How are you trying to run execute the scripts?

We recommend installing PiGx through GNU Guix[1], the reproducible package
manager.

[1]: https://gnu.org/s/guix

--
Ricardo Wurmus

System administrator
BIMSB - Scientific Bioinformatics Platform
Max Delbrueck Center for Molecular Medicine

Robert-Rössle-Str. 10, 13125, Berlin, Germany
Building 89, Room 1.08

email: ricardo...@mdc-berlin.de
tel: +49 30 9406 1796

[vin...@hkl.hms.harvard.edu]

I downloaded pigx-0.0.3.tar.gz

then ran the install like so:

./configure --prefix=/Users/jjv5/repos/pigx --enable-bsseq --enable-rnaseq --enable-scrnaseq --enable-chipseq --enable-crispr

This confirmed all dependencies (but didn't seem to check for cutadapt).

This also did not seem to install any pipelines.

My errors were my own fault and had nothing to do with pigx - pardon the bother. 

[Ricardo Wurmus]

vin...@hkl.hms.harvard.edu writes:

> I downloaded pigx-0.0.3.tar.gz
>
> then ran the install like so:
>
> ./configure --prefix=/Users/jjv5/repos/pigx --enable-bsseq --enable-rnaseq
> --enable-scrnaseq --enable-chipseq --enable-crispr

Okay, that’s good.

Be sure to also run “make” as some files need to be generated at build
time (as opposed to configure time); run “make install” to be sure that
embedded locations are resolved correctly.

(Otherwise you’d have to set the PIGX_UNINSTALLED environment variable,
which comes with a bunch of limitations that I suggest you better avoid.)

> My errors were my own fault and had nothing to do with pigx - pardon
> the bother.

No worries. I’m glad you figured it out!

--
Ricardo